anno_start	anno_end	anno_text	entity_type	sentence	section
9	16	cryo-EM	experimental_method	Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome	TITLE
26	34	inchworm	protein_state	Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome	TITLE
59	64	viral	taxonomy_domain	Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome	TITLE
65	69	IRES	site	Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome	TITLE
82	90	ribosome	complex_assembly	Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome	TITLE
0	29	Internal ribosome entry sites	site	Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs.	ABSTRACT
31	36	IRESs	site	Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs.	ABSTRACT
77	82	viral	taxonomy_domain	Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs.	ABSTRACT
83	88	mRNAs	chemical	Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs.	ABSTRACT
6	30	electron cryo-microscopy	experimental_method	Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin.	ABSTRACT
69	77	ribosome	complex_assembly	Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin.	ABSTRACT
78	88	structures	evidence	Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin.	ABSTRACT
105	125	Taura syndrome virus	species	Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin.	ABSTRACT
126	130	IRES	site	Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin.	ABSTRACT
135	146	translocase	protein_type	Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin.	ABSTRACT
147	155	eEF2•GTP	complex_assembly	Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin.	ABSTRACT
156	166	bound with	protein_state	Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin.	ABSTRACT
167	175	sordarin	chemical	Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin.	ABSTRACT
4	14	structures	evidence	The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics.	ABSTRACT
39	43	IRES	site	The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics.	ABSTRACT
84	94	initiation	protein_state	The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics.	ABSTRACT
133	137	eEF2	protein	The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics.	ABSTRACT
4	8	IRES	site	The IRES rearranges from extended to bent to extended conformations.	ABSTRACT
25	33	extended	protein_state	The IRES rearranges from extended to bent to extended conformations.	ABSTRACT
37	41	bent	protein_state	The IRES rearranges from extended to bent to extended conformations.	ABSTRACT
45	53	extended	protein_state	The IRES rearranges from extended to bent to extended conformations.	ABSTRACT
5	13	inchworm	protein_state	This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel.	ABSTRACT
81	84	40S	complex_assembly	This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel.	ABSTRACT
85	89	head	structure_element	This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel.	ABSTRACT
0	4	eEF2	protein	eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site.	ABSTRACT
22	25	60S	complex_assembly	eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site.	ABSTRACT
26	33	subunit	structure_element	eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site.	ABSTRACT
61	64	40S	complex_assembly	eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site.	ABSTRACT
65	72	subunit	structure_element	eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site.	ABSTRACT
65	72	subunit	structure_element	eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site.	ABSTRACT
86	92	A site	site	eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site.	ABSTRACT
4	15	diphthamide	ptm	Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center.	ABSTRACT
38	40	IV	structure_element	Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center.	ABSTRACT
55	82	tRNA-mRNA-like pseudoknot I	structure_element	Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center.	ABSTRACT
84	87	PKI	structure_element	Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center.	ABSTRACT
96	100	IRES	site	Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center.	ABSTRACT
110	125	decoding center	site	Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center.	ABSTRACT
13	16	40S	complex_assembly	This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites.	ABSTRACT
39	43	head	structure_element	This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites.	ABSTRACT
63	67	IRES	site	This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites.	ABSTRACT
122	125	PKI	structure_element	This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites.	ABSTRACT
147	160	A and P sites	site	This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites.	ABSTRACT
4	14	structures	evidence	The structures suggest missing links in our understanding of tRNA translocation.	ABSTRACT
61	65	tRNA	chemical	The structures suggest missing links in our understanding of tRNA translocation.	ABSTRACT
0	5	Virus	taxonomy_domain	Virus propagation relies on the host translational apparatus.	INTRO
33	38	mRNAs	chemical	To efficiently compete with host mRNAs and engage in translation under stress, some viral mRNAs undergo cap-independent translation.	INTRO
84	89	viral	taxonomy_domain	To efficiently compete with host mRNAs and engage in translation under stress, some viral mRNAs undergo cap-independent translation.	INTRO
90	95	mRNAs	chemical	To efficiently compete with host mRNAs and engage in translation under stress, some viral mRNAs undergo cap-independent translation.	INTRO
13	41	internal ribosome entry site	site	To this end, internal ribosome entry site (IRES) RNAs are employed (reviewed in.	INTRO
43	47	IRES	site	To this end, internal ribosome entry site (IRES) RNAs are employed (reviewed in.	INTRO
49	53	RNAs	chemical	To this end, internal ribosome entry site (IRES) RNAs are employed (reviewed in.	INTRO
3	7	IRES	site	An IRES is located at the 5’ untranslated region of the viral mRNA, preceding an open reading frame (ORF).	INTRO
26	48	5’ untranslated region	structure_element	An IRES is located at the 5’ untranslated region of the viral mRNA, preceding an open reading frame (ORF).	INTRO
56	61	viral	taxonomy_domain	An IRES is located at the 5’ untranslated region of the viral mRNA, preceding an open reading frame (ORF).	INTRO
62	66	mRNA	chemical	An IRES is located at the 5’ untranslated region of the viral mRNA, preceding an open reading frame (ORF).	INTRO
81	99	open reading frame	structure_element	An IRES is located at the 5’ untranslated region of the viral mRNA, preceding an open reading frame (ORF).	INTRO
101	104	ORF	structure_element	An IRES is located at the 5’ untranslated region of the viral mRNA, preceding an open reading frame (ORF).	INTRO
27	37	structured	protein_state	To initiate translation, a structured IRES RNA interacts with the 40S subunit or the 80S ribosome, resulting in precise positioning of the downstream start codon in the small 40S subunit.	INTRO
38	42	IRES	site	To initiate translation, a structured IRES RNA interacts with the 40S subunit or the 80S ribosome, resulting in precise positioning of the downstream start codon in the small 40S subunit.	INTRO
43	46	RNA	chemical	To initiate translation, a structured IRES RNA interacts with the 40S subunit or the 80S ribosome, resulting in precise positioning of the downstream start codon in the small 40S subunit.	INTRO
66	69	40S	complex_assembly	To initiate translation, a structured IRES RNA interacts with the 40S subunit or the 80S ribosome, resulting in precise positioning of the downstream start codon in the small 40S subunit.	INTRO
70	77	subunit	structure_element	To initiate translation, a structured IRES RNA interacts with the 40S subunit or the 80S ribosome, resulting in precise positioning of the downstream start codon in the small 40S subunit.	INTRO
85	97	80S ribosome	complex_assembly	To initiate translation, a structured IRES RNA interacts with the 40S subunit or the 80S ribosome, resulting in precise positioning of the downstream start codon in the small 40S subunit.	INTRO
169	174	small	protein_state	To initiate translation, a structured IRES RNA interacts with the 40S subunit or the 80S ribosome, resulting in precise positioning of the downstream start codon in the small 40S subunit.	INTRO
175	178	40S	complex_assembly	To initiate translation, a structured IRES RNA interacts with the 40S subunit or the 80S ribosome, resulting in precise positioning of the downstream start codon in the small 40S subunit.	INTRO
179	186	subunit	structure_element	To initiate translation, a structured IRES RNA interacts with the 40S subunit or the 80S ribosome, resulting in precise positioning of the downstream start codon in the small 40S subunit.	INTRO
44	48	IRES	site	The canonical scenario of cap-dependent and IRES-dependent initiation involves positioning of the AUG start codon and the initiator tRNAMet in the ribosomal peptidyl-tRNA (P) site, facilitated by interaction with initiation factors.	INTRO
132	139	tRNAMet	chemical	The canonical scenario of cap-dependent and IRES-dependent initiation involves positioning of the AUG start codon and the initiator tRNAMet in the ribosomal peptidyl-tRNA (P) site, facilitated by interaction with initiation factors.	INTRO
157	179	peptidyl-tRNA (P) site	site	The canonical scenario of cap-dependent and IRES-dependent initiation involves positioning of the AUG start codon and the initiator tRNAMet in the ribosomal peptidyl-tRNA (P) site, facilitated by interaction with initiation factors.	INTRO
213	231	initiation factors	protein_type	The canonical scenario of cap-dependent and IRES-dependent initiation involves positioning of the AUG start codon and the initiator tRNAMet in the ribosomal peptidyl-tRNA (P) site, facilitated by interaction with initiation factors.	INTRO
35	49	aminoacyl-tRNA	chemical	Subsequent binding of an elongator aminoacyl-tRNA to the ribosomal A site transitions the initiation complex into the elongation cycle of translation.	INTRO
67	73	A site	site	Subsequent binding of an elongator aminoacyl-tRNA to the ribosomal A site transitions the initiation complex into the elongation cycle of translation.	INTRO
90	108	initiation complex	complex_assembly	Subsequent binding of an elongator aminoacyl-tRNA to the ribosomal A site transitions the initiation complex into the elongation cycle of translation.	INTRO
37	42	tRNAs	chemical	Upon peptide bond formation, the two tRNAs and their respective mRNA codons translocate from the A and P to P and E (exit) sites, freeing the A site for the next elongator tRNA.	INTRO
64	68	mRNA	chemical	Upon peptide bond formation, the two tRNAs and their respective mRNA codons translocate from the A and P to P and E (exit) sites, freeing the A site for the next elongator tRNA.	INTRO
97	104	A and P	site	Upon peptide bond formation, the two tRNAs and their respective mRNA codons translocate from the A and P to P and E (exit) sites, freeing the A site for the next elongator tRNA.	INTRO
108	128	P and E (exit) sites	site	Upon peptide bond formation, the two tRNAs and their respective mRNA codons translocate from the A and P to P and E (exit) sites, freeing the A site for the next elongator tRNA.	INTRO
142	148	A site	site	Upon peptide bond formation, the two tRNAs and their respective mRNA codons translocate from the A and P to P and E (exit) sites, freeing the A site for the next elongator tRNA.	INTRO
172	176	tRNA	chemical	Upon peptide bond formation, the two tRNAs and their respective mRNA codons translocate from the A and P to P and E (exit) sites, freeing the A site for the next elongator tRNA.	INTRO
23	33	initiation	protein_state	An unusual strategy of initiation is used by intergenic-region (IGR) IRESs found in Dicistroviridae arthropod-infecting viruses.	INTRO
45	62	intergenic-region	structure_element	An unusual strategy of initiation is used by intergenic-region (IGR) IRESs found in Dicistroviridae arthropod-infecting viruses.	INTRO
64	67	IGR	structure_element	An unusual strategy of initiation is used by intergenic-region (IGR) IRESs found in Dicistroviridae arthropod-infecting viruses.	INTRO
69	74	IRESs	site	An unusual strategy of initiation is used by intergenic-region (IGR) IRESs found in Dicistroviridae arthropod-infecting viruses.	INTRO
84	109	Dicistroviridae arthropod	species	An unusual strategy of initiation is used by intergenic-region (IGR) IRESs found in Dicistroviridae arthropod-infecting viruses.	INTRO
120	127	viruses	taxonomy_domain	An unusual strategy of initiation is used by intergenic-region (IGR) IRESs found in Dicistroviridae arthropod-infecting viruses.	INTRO
14	20	shrimp	taxonomy_domain	These include shrimp-infecting Taura syndrome virus (TSV), and insect viruses Plautia stali intestine virus (PSIV) and Cricket paralysis virus (CrPV).	INTRO
31	51	Taura syndrome virus	species	These include shrimp-infecting Taura syndrome virus (TSV), and insect viruses Plautia stali intestine virus (PSIV) and Cricket paralysis virus (CrPV).	INTRO
53	56	TSV	species	These include shrimp-infecting Taura syndrome virus (TSV), and insect viruses Plautia stali intestine virus (PSIV) and Cricket paralysis virus (CrPV).	INTRO
63	69	insect	taxonomy_domain	These include shrimp-infecting Taura syndrome virus (TSV), and insect viruses Plautia stali intestine virus (PSIV) and Cricket paralysis virus (CrPV).	INTRO
78	107	Plautia stali intestine virus	species	These include shrimp-infecting Taura syndrome virus (TSV), and insect viruses Plautia stali intestine virus (PSIV) and Cricket paralysis virus (CrPV).	INTRO
109	113	PSIV	species	These include shrimp-infecting Taura syndrome virus (TSV), and insect viruses Plautia stali intestine virus (PSIV) and Cricket paralysis virus (CrPV).	INTRO
119	142	Cricket paralysis virus	species	These include shrimp-infecting Taura syndrome virus (TSV), and insect viruses Plautia stali intestine virus (PSIV) and Cricket paralysis virus (CrPV).	INTRO
144	148	CrPV	species	These include shrimp-infecting Taura syndrome virus (TSV), and insect viruses Plautia stali intestine virus (PSIV) and Cricket paralysis virus (CrPV).	INTRO
4	7	IGR	structure_element	The IGR IRES mRNAs do not contain an AUG start codon.	INTRO
8	12	IRES	site	The IGR IRES mRNAs do not contain an AUG start codon.	INTRO
13	18	mRNAs	chemical	The IGR IRES mRNAs do not contain an AUG start codon.	INTRO
4	7	IGR	structure_element	The IGR-IRES-driven initiation does not involve initiator tRNAMet and initiation factors.	INTRO
8	12	IRES	site	The IGR-IRES-driven initiation does not involve initiator tRNAMet and initiation factors.	INTRO
20	30	initiation	protein_state	The IGR-IRES-driven initiation does not involve initiator tRNAMet and initiation factors.	INTRO
58	65	tRNAMet	chemical	The IGR-IRES-driven initiation does not involve initiator tRNAMet and initiation factors.	INTRO
70	80	initiation	protein_state	The IGR-IRES-driven initiation does not involve initiator tRNAMet and initiation factors.	INTRO
23	28	IRESs	site	As such, this group of IRESs represents the most streamlined mechanism of eukaryotic translation initiation.	INTRO
74	84	eukaryotic	taxonomy_domain	As such, this group of IRESs represents the most streamlined mechanism of eukaryotic translation initiation.	INTRO
97	107	initiation	protein_state	As such, this group of IRESs represents the most streamlined mechanism of eukaryotic translation initiation.	INTRO
26	35	bacterial	taxonomy_domain	A recent demonstration of bacterial translation initiation by an IGR IRES indicates that the IRESs take advantage of conserved structural and dynamic properties of the ribosome.	INTRO
48	58	initiation	protein_state	A recent demonstration of bacterial translation initiation by an IGR IRES indicates that the IRESs take advantage of conserved structural and dynamic properties of the ribosome.	INTRO
65	68	IGR	structure_element	A recent demonstration of bacterial translation initiation by an IGR IRES indicates that the IRESs take advantage of conserved structural and dynamic properties of the ribosome.	INTRO
69	73	IRES	site	A recent demonstration of bacterial translation initiation by an IGR IRES indicates that the IRESs take advantage of conserved structural and dynamic properties of the ribosome.	INTRO
93	98	IRESs	site	A recent demonstration of bacterial translation initiation by an IGR IRES indicates that the IRESs take advantage of conserved structural and dynamic properties of the ribosome.	INTRO
168	176	ribosome	complex_assembly	A recent demonstration of bacterial translation initiation by an IGR IRES indicates that the IRESs take advantage of conserved structural and dynamic properties of the ribosome.	INTRO
6	30	electron cryo-microscopy	experimental_method	Early electron cryo-microscopy (cryo-EM) studies have found that the CrPV IRES packs in the ribosome intersubunit space.	INTRO
32	39	cryo-EM	experimental_method	Early electron cryo-microscopy (cryo-EM) studies have found that the CrPV IRES packs in the ribosome intersubunit space.	INTRO
69	73	CrPV	species	Early electron cryo-microscopy (cryo-EM) studies have found that the CrPV IRES packs in the ribosome intersubunit space.	INTRO
74	78	IRES	site	Early electron cryo-microscopy (cryo-EM) studies have found that the CrPV IRES packs in the ribosome intersubunit space.	INTRO
92	100	ribosome	complex_assembly	Early electron cryo-microscopy (cryo-EM) studies have found that the CrPV IRES packs in the ribosome intersubunit space.	INTRO
101	119	intersubunit space	site	Early electron cryo-microscopy (cryo-EM) studies have found that the CrPV IRES packs in the ribosome intersubunit space.	INTRO
7	14	cryo-EM	experimental_method	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
15	25	structures	evidence	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
29	43	ribosome-bound	protein_state	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
44	47	TSV	species	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
48	52	IRES	site	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
57	61	CrPV	species	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
62	66	IRES	site	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
81	84	IGR	structure_element	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
85	90	IRESs	site	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
104	107	ORF	structure_element	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
135	143	ribosome	complex_assembly	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
144	154	bound with	protein_state	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
155	159	tRNA	chemical	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
164	168	mRNA	chemical	Recent cryo-EM structures of ribosome-bound TSV IRES and CrPV IRES revealed that IGR IRESs position the ORF by mimicking a translating ribosome bound with tRNA and mRNA.	INTRO
12	16	IRES	site	The ~200-nt IRES RNAs span from the A site beyond the E site.	INTRO
17	21	RNAs	chemical	The ~200-nt IRES RNAs span from the A site beyond the E site.	INTRO
36	42	A site	site	The ~200-nt IRES RNAs span from the A site beyond the E site.	INTRO
54	60	E site	site	The ~200-nt IRES RNAs span from the A site beyond the E site.	INTRO
2	11	conserved	protein_state	A conserved tRNA-mRNA–like structural element of pseudoknot I (PKI) interacts with the decoding center in the A site of the 40S subunit.	INTRO
12	45	tRNA-mRNA–like structural element	structure_element	A conserved tRNA-mRNA–like structural element of pseudoknot I (PKI) interacts with the decoding center in the A site of the 40S subunit.	INTRO
49	61	pseudoknot I	structure_element	A conserved tRNA-mRNA–like structural element of pseudoknot I (PKI) interacts with the decoding center in the A site of the 40S subunit.	INTRO
63	66	PKI	structure_element	A conserved tRNA-mRNA–like structural element of pseudoknot I (PKI) interacts with the decoding center in the A site of the 40S subunit.	INTRO
87	102	decoding center	site	A conserved tRNA-mRNA–like structural element of pseudoknot I (PKI) interacts with the decoding center in the A site of the 40S subunit.	INTRO
110	116	A site	site	A conserved tRNA-mRNA–like structural element of pseudoknot I (PKI) interacts with the decoding center in the A site of the 40S subunit.	INTRO
124	127	40S	complex_assembly	A conserved tRNA-mRNA–like structural element of pseudoknot I (PKI) interacts with the decoding center in the A site of the 40S subunit.	INTRO
128	135	subunit	structure_element	A conserved tRNA-mRNA–like structural element of pseudoknot I (PKI) interacts with the decoding center in the A site of the 40S subunit.	INTRO
4	30	codon-anticodon-like helix	structure_element	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
34	37	PKI	structure_element	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
77	98	universally conserved	protein_state	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
99	114	decoding-center	site	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
127	131	G577	residue_name_number	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
133	138	A1755	residue_name_number	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
143	148	A1756	residue_name_number	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
150	154	G530	residue_name_number	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
156	161	A1492	residue_name_number	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
166	171	A1493	residue_name_number	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
175	182	E. coli	species	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
197	200	RNA	chemical	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
205	209	rRNA	chemical	The codon-anticodon-like helix of PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 (G530, A1492 and A1493 in E. coli 16S ribosomal RNA, or rRNA).	INTRO
43	50	alanine	residue_name	The downstream initiation codon—coding for alanine—is placed in the mRNA tunnel, preceding the decoding center.	INTRO
68	79	mRNA tunnel	site	The downstream initiation codon—coding for alanine—is placed in the mRNA tunnel, preceding the decoding center.	INTRO
95	110	decoding center	site	The downstream initiation codon—coding for alanine—is placed in the mRNA tunnel, preceding the decoding center.	INTRO
0	3	PKI	structure_element	PKI of IGR IRESs therefore mimics an A-site elongator tRNA interacting with an mRNA sense codon, but not a P-site initiator tRNAMet and the AUG start codon.	INTRO
7	10	IGR	structure_element	PKI of IGR IRESs therefore mimics an A-site elongator tRNA interacting with an mRNA sense codon, but not a P-site initiator tRNAMet and the AUG start codon.	INTRO
11	16	IRESs	site	PKI of IGR IRESs therefore mimics an A-site elongator tRNA interacting with an mRNA sense codon, but not a P-site initiator tRNAMet and the AUG start codon.	INTRO
37	43	A-site	site	PKI of IGR IRESs therefore mimics an A-site elongator tRNA interacting with an mRNA sense codon, but not a P-site initiator tRNAMet and the AUG start codon.	INTRO
54	58	tRNA	chemical	PKI of IGR IRESs therefore mimics an A-site elongator tRNA interacting with an mRNA sense codon, but not a P-site initiator tRNAMet and the AUG start codon.	INTRO
79	83	mRNA	chemical	PKI of IGR IRESs therefore mimics an A-site elongator tRNA interacting with an mRNA sense codon, but not a P-site initiator tRNAMet and the AUG start codon.	INTRO
107	113	P-site	site	PKI of IGR IRESs therefore mimics an A-site elongator tRNA interacting with an mRNA sense codon, but not a P-site initiator tRNAMet and the AUG start codon.	INTRO
124	131	tRNAMet	chemical	PKI of IGR IRESs therefore mimics an A-site elongator tRNA interacting with an mRNA sense codon, but not a P-site initiator tRNAMet and the AUG start codon.	INTRO
23	33	initiation	protein_state	How this non-canonical initiation complex transitions to the elongation step is not fully understood.	INTRO
14	28	aminoacyl-tRNA	chemical	For a cognate aminoacyl-tRNA to bind the first viral mRNA codon, PKI has to be translocated from the A site, so that the first codon can be presented in the A site.	INTRO
47	52	viral	taxonomy_domain	For a cognate aminoacyl-tRNA to bind the first viral mRNA codon, PKI has to be translocated from the A site, so that the first codon can be presented in the A site.	INTRO
53	57	mRNA	chemical	For a cognate aminoacyl-tRNA to bind the first viral mRNA codon, PKI has to be translocated from the A site, so that the first codon can be presented in the A site.	INTRO
65	68	PKI	structure_element	For a cognate aminoacyl-tRNA to bind the first viral mRNA codon, PKI has to be translocated from the A site, so that the first codon can be presented in the A site.	INTRO
101	107	A site	site	For a cognate aminoacyl-tRNA to bind the first viral mRNA codon, PKI has to be translocated from the A site, so that the first codon can be presented in the A site.	INTRO
157	163	A site	site	For a cognate aminoacyl-tRNA to bind the first viral mRNA codon, PKI has to be translocated from the A site, so that the first codon can be presented in the A site.	INTRO
2	9	cryo-EM	experimental_method	A cryo-EM structure of the ribosome bound with a CrPV IRES and release factor eRF1 occupying the A site provided insight into the post-translocation state.	INTRO
10	19	structure	evidence	A cryo-EM structure of the ribosome bound with a CrPV IRES and release factor eRF1 occupying the A site provided insight into the post-translocation state.	INTRO
27	35	ribosome	complex_assembly	A cryo-EM structure of the ribosome bound with a CrPV IRES and release factor eRF1 occupying the A site provided insight into the post-translocation state.	INTRO
36	46	bound with	protein_state	A cryo-EM structure of the ribosome bound with a CrPV IRES and release factor eRF1 occupying the A site provided insight into the post-translocation state.	INTRO
49	53	CrPV	species	A cryo-EM structure of the ribosome bound with a CrPV IRES and release factor eRF1 occupying the A site provided insight into the post-translocation state.	INTRO
54	58	IRES	site	A cryo-EM structure of the ribosome bound with a CrPV IRES and release factor eRF1 occupying the A site provided insight into the post-translocation state.	INTRO
63	77	release factor	protein_type	A cryo-EM structure of the ribosome bound with a CrPV IRES and release factor eRF1 occupying the A site provided insight into the post-translocation state.	INTRO
78	82	eRF1	protein	A cryo-EM structure of the ribosome bound with a CrPV IRES and release factor eRF1 occupying the A site provided insight into the post-translocation state.	INTRO
97	103	A site	site	A cryo-EM structure of the ribosome bound with a CrPV IRES and release factor eRF1 occupying the A site provided insight into the post-translocation state.	INTRO
130	148	post-translocation	protein_state	A cryo-EM structure of the ribosome bound with a CrPV IRES and release factor eRF1 occupying the A site provided insight into the post-translocation state.	INTRO
8	17	structure	evidence	In this structure, PKI is positioned in the P site and the first mRNA codon is located in the A site.	INTRO
19	22	PKI	structure_element	In this structure, PKI is positioned in the P site and the first mRNA codon is located in the A site.	INTRO
44	50	P site	site	In this structure, PKI is positioned in the P site and the first mRNA codon is located in the A site.	INTRO
65	69	mRNA	chemical	In this structure, PKI is positioned in the P site and the first mRNA codon is located in the A site.	INTRO
94	100	A site	site	In this structure, PKI is positioned in the P site and the first mRNA codon is located in the A site.	INTRO
8	13	large	protein_state	How the large IRES RNA translocates within the ribosome, allowing PKI translocation from the A to P site is not known.	INTRO
14	18	IRES	site	How the large IRES RNA translocates within the ribosome, allowing PKI translocation from the A to P site is not known.	INTRO
19	22	RNA	chemical	How the large IRES RNA translocates within the ribosome, allowing PKI translocation from the A to P site is not known.	INTRO
47	55	ribosome	complex_assembly	How the large IRES RNA translocates within the ribosome, allowing PKI translocation from the A to P site is not known.	INTRO
66	69	PKI	structure_element	How the large IRES RNA translocates within the ribosome, allowing PKI translocation from the A to P site is not known.	INTRO
93	104	A to P site	site	How the large IRES RNA translocates within the ribosome, allowing PKI translocation from the A to P site is not known.	INTRO
29	32	PKI	structure_element	The structural similarity of PKI and the tRNA anticodon stem loop (ASL) bound to a codon suggests that their mechanisms of translocation are similar to some extent.	INTRO
41	45	tRNA	chemical	The structural similarity of PKI and the tRNA anticodon stem loop (ASL) bound to a codon suggests that their mechanisms of translocation are similar to some extent.	INTRO
46	65	anticodon stem loop	structure_element	The structural similarity of PKI and the tRNA anticodon stem loop (ASL) bound to a codon suggests that their mechanisms of translocation are similar to some extent.	INTRO
67	70	ASL	structure_element	The structural similarity of PKI and the tRNA anticodon stem loop (ASL) bound to a codon suggests that their mechanisms of translocation are similar to some extent.	INTRO
72	80	bound to	protein_state	The structural similarity of PKI and the tRNA anticodon stem loop (ASL) bound to a codon suggests that their mechanisms of translocation are similar to some extent.	INTRO
21	25	IRES	site	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
29	38	tRNA-mRNA	complex_assembly	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
48	58	eukaryotic	taxonomy_domain	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
59	78	elongation factor 2	protein	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
80	84	eEF2	protein	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
143	152	bacterial	taxonomy_domain	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
153	157	EF-G	protein	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
159	176	Pre-translocation	protein_state	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
177	187	tRNA-bound	protein_state	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
188	197	ribosomes	complex_assembly	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
208	233	peptidyl- and deacyl-tRNA	chemical	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
255	259	mRNA	chemical	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
274	287	A and P sites	site	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
296	306	2tRNA•mRNA	complex_assembly	Translocation of the IRES or tRNA-mRNA requires eukaryotic elongation factor 2 (eEF2), a structural and functional homolog of the well-studied bacterial EF-G. Pre-translocation tRNA-bound ribosomes contain a peptidyl- and deacyl-tRNA, both base-paired to mRNA codons in the A and P sites (termed 2tRNA•mRNA complex).	INTRO
17	27	2tRNA•mRNA	complex_assembly	Translocation of 2tRNA•mRNA involves two major large-scale ribosome rearrangements (Figure 1—figure supplement 1) (reviewed in).	INTRO
59	67	ribosome	complex_assembly	Translocation of 2tRNA•mRNA involves two major large-scale ribosome rearrangements (Figure 1—figure supplement 1) (reviewed in).	INTRO
18	27	bacterial	taxonomy_domain	First, studies of bacterial ribosomes showed that a ~10° rotation of the small subunit relative to the large subunit, known as intersubunit rotation, or ratcheting, is required for translocation.	INTRO
28	37	ribosomes	complex_assembly	First, studies of bacterial ribosomes showed that a ~10° rotation of the small subunit relative to the large subunit, known as intersubunit rotation, or ratcheting, is required for translocation.	INTRO
73	86	small subunit	structure_element	First, studies of bacterial ribosomes showed that a ~10° rotation of the small subunit relative to the large subunit, known as intersubunit rotation, or ratcheting, is required for translocation.	INTRO
103	116	large subunit	structure_element	First, studies of bacterial ribosomes showed that a ~10° rotation of the small subunit relative to the large subunit, known as intersubunit rotation, or ratcheting, is required for translocation.	INTRO
100	106	hybrid	protein_state	Intersubunit rotation occurs spontaneously upon peptidyl transfer, and is coupled with formation of hybrid tRNA states.	INTRO
107	111	tRNA	chemical	Intersubunit rotation occurs spontaneously upon peptidyl transfer, and is coupled with formation of hybrid tRNA states.	INTRO
7	14	rotated	protein_state	In the rotated pre-translocation ribosome, the peptidyl-tRNA binds the A site of the small subunit with its ASL and the P site of the large subunit with the CCA 3’ end (A/P hybrid state).	INTRO
15	32	pre-translocation	protein_state	In the rotated pre-translocation ribosome, the peptidyl-tRNA binds the A site of the small subunit with its ASL and the P site of the large subunit with the CCA 3’ end (A/P hybrid state).	INTRO
33	41	ribosome	complex_assembly	In the rotated pre-translocation ribosome, the peptidyl-tRNA binds the A site of the small subunit with its ASL and the P site of the large subunit with the CCA 3’ end (A/P hybrid state).	INTRO
47	60	peptidyl-tRNA	chemical	In the rotated pre-translocation ribosome, the peptidyl-tRNA binds the A site of the small subunit with its ASL and the P site of the large subunit with the CCA 3’ end (A/P hybrid state).	INTRO
71	77	A site	site	In the rotated pre-translocation ribosome, the peptidyl-tRNA binds the A site of the small subunit with its ASL and the P site of the large subunit with the CCA 3’ end (A/P hybrid state).	INTRO
85	98	small subunit	structure_element	In the rotated pre-translocation ribosome, the peptidyl-tRNA binds the A site of the small subunit with its ASL and the P site of the large subunit with the CCA 3’ end (A/P hybrid state).	INTRO
108	111	ASL	structure_element	In the rotated pre-translocation ribosome, the peptidyl-tRNA binds the A site of the small subunit with its ASL and the P site of the large subunit with the CCA 3’ end (A/P hybrid state).	INTRO
120	126	P site	site	In the rotated pre-translocation ribosome, the peptidyl-tRNA binds the A site of the small subunit with its ASL and the P site of the large subunit with the CCA 3’ end (A/P hybrid state).	INTRO
134	147	large subunit	structure_element	In the rotated pre-translocation ribosome, the peptidyl-tRNA binds the A site of the small subunit with its ASL and the P site of the large subunit with the CCA 3’ end (A/P hybrid state).	INTRO
169	179	A/P hybrid	protein_state	In the rotated pre-translocation ribosome, the peptidyl-tRNA binds the A site of the small subunit with its ASL and the P site of the large subunit with the CCA 3’ end (A/P hybrid state).	INTRO
18	29	deacyl-tRNA	chemical	Concurrently, the deacyl-tRNA interacts with the P site of the small subunit and the E site of the large subunit (P/E hybrid state).	INTRO
49	55	P site	site	Concurrently, the deacyl-tRNA interacts with the P site of the small subunit and the E site of the large subunit (P/E hybrid state).	INTRO
63	76	small subunit	structure_element	Concurrently, the deacyl-tRNA interacts with the P site of the small subunit and the E site of the large subunit (P/E hybrid state).	INTRO
85	91	E site	site	Concurrently, the deacyl-tRNA interacts with the P site of the small subunit and the E site of the large subunit (P/E hybrid state).	INTRO
99	112	large subunit	structure_element	Concurrently, the deacyl-tRNA interacts with the P site of the small subunit and the E site of the large subunit (P/E hybrid state).	INTRO
114	124	P/E hybrid	protein_state	Concurrently, the deacyl-tRNA interacts with the P site of the small subunit and the E site of the large subunit (P/E hybrid state).	INTRO
4	12	ribosome	complex_assembly	The ribosome can undergo spontaneous, thermally-driven forward-reverse rotation that shifts the two tRNAs between the hybrid and 'classical' states while the anticodon stem loops remain non-translocated.	INTRO
100	105	tRNAs	chemical	The ribosome can undergo spontaneous, thermally-driven forward-reverse rotation that shifts the two tRNAs between the hybrid and 'classical' states while the anticodon stem loops remain non-translocated.	INTRO
118	124	hybrid	protein_state	The ribosome can undergo spontaneous, thermally-driven forward-reverse rotation that shifts the two tRNAs between the hybrid and 'classical' states while the anticodon stem loops remain non-translocated.	INTRO
130	139	classical	protein_state	The ribosome can undergo spontaneous, thermally-driven forward-reverse rotation that shifts the two tRNAs between the hybrid and 'classical' states while the anticodon stem loops remain non-translocated.	INTRO
158	178	anticodon stem loops	structure_element	The ribosome can undergo spontaneous, thermally-driven forward-reverse rotation that shifts the two tRNAs between the hybrid and 'classical' states while the anticodon stem loops remain non-translocated.	INTRO
186	202	non-translocated	protein_state	The ribosome can undergo spontaneous, thermally-driven forward-reverse rotation that shifts the two tRNAs between the hybrid and 'classical' states while the anticodon stem loops remain non-translocated.	INTRO
11	15	EF-G	protein	Binding of EF-G next to the A site and reverse rotation of the small subunit results in translocation of both ASLs on the small subunit.	INTRO
28	34	A site	site	Binding of EF-G next to the A site and reverse rotation of the small subunit results in translocation of both ASLs on the small subunit.	INTRO
63	76	small subunit	structure_element	Binding of EF-G next to the A site and reverse rotation of the small subunit results in translocation of both ASLs on the small subunit.	INTRO
110	114	ASLs	structure_element	Binding of EF-G next to the A site and reverse rotation of the small subunit results in translocation of both ASLs on the small subunit.	INTRO
122	135	small subunit	structure_element	Binding of EF-G next to the A site and reverse rotation of the small subunit results in translocation of both ASLs on the small subunit.	INTRO
0	4	EF-G	protein	EF-G is thought to 'unlock' the pre-translocation ribosome, allowing movement of the 2tRNA•mRNA complex, however the structural details of this unlocking are not known.	INTRO
32	49	pre-translocation	protein_state	EF-G is thought to 'unlock' the pre-translocation ribosome, allowing movement of the 2tRNA•mRNA complex, however the structural details of this unlocking are not known.	INTRO
50	58	ribosome	complex_assembly	EF-G is thought to 'unlock' the pre-translocation ribosome, allowing movement of the 2tRNA•mRNA complex, however the structural details of this unlocking are not known.	INTRO
85	95	2tRNA•mRNA	complex_assembly	EF-G is thought to 'unlock' the pre-translocation ribosome, allowing movement of the 2tRNA•mRNA complex, however the structural details of this unlocking are not known.	INTRO
77	81	head	structure_element	The second large-scale rearrangement involves rotation, or swiveling, of the head of the small subunit relative to the body.	INTRO
89	102	small subunit	structure_element	The second large-scale rearrangement involves rotation, or swiveling, of the head of the small subunit relative to the body.	INTRO
119	123	body	structure_element	The second large-scale rearrangement involves rotation, or swiveling, of the head of the small subunit relative to the body.	INTRO
4	8	head	structure_element	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
109	119	absence of	protein_state	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
120	124	tRNA	chemical	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
135	146	presence of	protein_state	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
156	157	P	site	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
158	159	E	site	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
160	164	tRNA	chemical	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
169	173	eEF2	protein	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
177	181	EF-G	protein	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
183	216	Förster resonance energy transfer	experimental_method	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
218	222	FRET	experimental_method	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
242	246	head	structure_element	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
261	268	rotated	protein_state	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
269	282	small subunit	structure_element	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
295	299	EF-G	protein	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
321	331	2tRNA•mRNA	complex_assembly	The head can rotate by up to ~20° around the axis nearly orthogonal to that of intersubunit rotation, in the absence of tRNA or in the presence of a single P/E tRNA and eEF2 or EF-G. Förster resonance energy transfer (FRET) data suggest that head swivel of the rotated small subunit facilitates EF-G-mediated movement of 2tRNA•mRNA.	INTRO
0	10	Structures	evidence	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
18	26	70S•EF-G	complex_assembly	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
35	45	bound with	protein_state	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
50	69	nearly translocated	protein_state	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
70	75	tRNAs	chemical	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
104	108	head	structure_element	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
121	132	mid-rotated	protein_state	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
133	140	subunit	structure_element	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
153	157	head	structure_element	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
184	197	fully rotated	protein_state	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
198	215	pre-translocation	protein_state	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
226	237	non-rotated	protein_state	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
238	256	post-translocation	protein_state	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
257	271	70S•2tRNA•EF-G	complex_assembly	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
272	282	structures	evidence	Structures of the 70S•EF-G complex bound with two nearly translocated tRNAs, exhibit a large 18° to 21° head swivel in a mid-rotated subunit, whereas no head swivel is observed in the fully rotated pre-translocation or in the non-rotated post-translocation 70S•2tRNA•EF-G structures.	INTRO
23	27	head	structure_element	The structural role of head swivel is not fully understood.	INTRO
4	8	head	structure_element	The head swivel was proposed to facilitate transition of the tRNA from the P to E site by widening a constriction between these sites on the 30S subunit.	INTRO
61	65	tRNA	chemical	The head swivel was proposed to facilitate transition of the tRNA from the P to E site by widening a constriction between these sites on the 30S subunit.	INTRO
75	86	P to E site	site	The head swivel was proposed to facilitate transition of the tRNA from the P to E site by widening a constriction between these sites on the 30S subunit.	INTRO
101	113	constriction	site	The head swivel was proposed to facilitate transition of the tRNA from the P to E site by widening a constriction between these sites on the 30S subunit.	INTRO
141	144	30S	complex_assembly	The head swivel was proposed to facilitate transition of the tRNA from the P to E site by widening a constriction between these sites on the 30S subunit.	INTRO
145	152	subunit	structure_element	The head swivel was proposed to facilitate transition of the tRNA from the P to E site by widening a constriction between these sites on the 30S subunit.	INTRO
145	152	subunit	structure_element	The head swivel was proposed to facilitate transition of the tRNA from the P to E site by widening a constriction between these sites on the 30S subunit.	INTRO
25	28	ASL	structure_element	This widening allows the ASL to sample positions between the P and E sites.	INTRO
61	74	P and E sites	site	This widening allows the ASL to sample positions between the P and E sites.	INTRO
20	24	head	structure_element	Whether and how the head swivel mediates tRNA transition from the A to P site remains unknown.	INTRO
41	45	tRNA	chemical	Whether and how the head swivel mediates tRNA transition from the A to P site remains unknown.	INTRO
66	77	A to P site	site	Whether and how the head swivel mediates tRNA transition from the A to P site remains unknown.	INTRO
14	28	70S•2tRNA•mRNA	complex_assembly	Comparison of 70S•2tRNA•mRNA and 80S•IRES translocation complexes.	FIG
33	41	80S•IRES	complex_assembly	Comparison of 70S•2tRNA•mRNA and 80S•IRES translocation complexes.	FIG
4	14	Structures	evidence	(a) Structures of bacterial 70S•2tRNA•mRNA translocation complexes, ordered according to the position of the translocating A->P tRNA (orange).	FIG
18	27	bacterial	taxonomy_domain	(a) Structures of bacterial 70S•2tRNA•mRNA translocation complexes, ordered according to the position of the translocating A->P tRNA (orange).	FIG
28	42	70S•2tRNA•mRNA	complex_assembly	(a) Structures of bacterial 70S•2tRNA•mRNA translocation complexes, ordered according to the position of the translocating A->P tRNA (orange).	FIG
123	127	A->P	site	(a) Structures of bacterial 70S•2tRNA•mRNA translocation complexes, ordered according to the position of the translocating A->P tRNA (orange).	FIG
128	132	tRNA	chemical	(a) Structures of bacterial 70S•2tRNA•mRNA translocation complexes, ordered according to the position of the translocating A->P tRNA (orange).	FIG
20	27	subunit	structure_element	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body), elongation factor G (EF-G) is shown in green.	FIG
50	63	small subunit	structure_element	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body), elongation factor G (EF-G) is shown in green.	FIG
81	85	head	structure_element	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body), elongation factor G (EF-G) is shown in green.	FIG
105	109	body	structure_element	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body), elongation factor G (EF-G) is shown in green.	FIG
112	131	elongation factor G	protein	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body), elongation factor G (EF-G) is shown in green.	FIG
133	137	EF-G	protein	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body), elongation factor G (EF-G) is shown in green.	FIG
12	17	C1054	residue_name_number	Nucleotides C1054, G966 and G693 of 16S rRNA are shown in black to denote the A, P and E sites, respectively.	FIG
19	23	G966	residue_name_number	Nucleotides C1054, G966 and G693 of 16S rRNA are shown in black to denote the A, P and E sites, respectively.	FIG
28	32	G693	residue_name_number	Nucleotides C1054, G966 and G693 of 16S rRNA are shown in black to denote the A, P and E sites, respectively.	FIG
36	44	16S rRNA	chemical	Nucleotides C1054, G966 and G693 of 16S rRNA are shown in black to denote the A, P and E sites, respectively.	FIG
78	94	A, P and E sites	site	Nucleotides C1054, G966 and G693 of 16S rRNA are shown in black to denote the A, P and E sites, respectively.	FIG
19	22	30S	complex_assembly	The extents of the 30S subunit rotation and head swivel relative to their positions in the post-translocation structure are shown with arrows.	FIG
23	30	subunit	structure_element	The extents of the 30S subunit rotation and head swivel relative to their positions in the post-translocation structure are shown with arrows.	FIG
44	48	head	structure_element	The extents of the 30S subunit rotation and head swivel relative to their positions in the post-translocation structure are shown with arrows.	FIG
91	109	post-translocation	protein_state	The extents of the 30S subunit rotation and head swivel relative to their positions in the post-translocation structure are shown with arrows.	FIG
110	119	structure	evidence	The extents of the 30S subunit rotation and head swivel relative to their positions in the post-translocation structure are shown with arrows.	FIG
32	42	structures	evidence	References and PDB codes of the structures are shown.	FIG
4	14	Structures	evidence	(b) Structures of the 80S•IRES complexes in the absence and presence of eEF2 (this work).	FIG
22	30	80S•IRES	complex_assembly	(b) Structures of the 80S•IRES complexes in the absence and presence of eEF2 (this work).	FIG
48	55	absence	protein_state	(b) Structures of the 80S•IRES complexes in the absence and presence of eEF2 (this work).	FIG
60	71	presence of	protein_state	(b) Structures of the 80S•IRES complexes in the absence and presence of eEF2 (this work).	FIG
72	76	eEF2	protein	(b) Structures of the 80S•IRES complexes in the absence and presence of eEF2 (this work).	FIG
20	27	subunit	structure_element	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
50	63	small subunit	structure_element	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
81	85	head	structure_element	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
105	109	body	structure_element	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
116	119	TSV	species	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
120	124	IRES	site	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
133	137	eEF2	protein	The large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
12	17	C1274	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
19	24	U1191	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
32	35	40S	complex_assembly	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
36	40	head	structure_element	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
45	49	G904	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
57	65	platform	structure_element	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
84	89	C1054	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
91	95	G966	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
100	104	G693	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
108	115	E. coli	species	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
116	124	16S rRNA	chemical	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
159	175	A, P and E sites	site	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (corresponding to C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
26	30	IRES	site	Unresolved regions of the IRES in densities for Structures III and V are shown in gray.	FIG
34	43	densities	evidence	Unresolved regions of the IRES in densities for Structures III and V are shown in gray.	FIG
48	68	Structures III and V	evidence	Unresolved regions of the IRES in densities for Structures III and V are shown in gray.	FIG
26	30	IRES	site	Unresolved regions of the IRES in densities for Structures III and V are shown in gray.	FIG
34	43	densities	evidence	Unresolved regions of the IRES in densities for Structures III and V are shown in gray.	FIG
48	68	Structures III and V	evidence	Unresolved regions of the IRES in densities for Structures III and V are shown in gray.	FIG
19	22	40S	complex_assembly	The extents of the 40S subunit rotation and head swivel relative to their positions in the post-translocation structure are shown with arrows.	FIG
23	30	subunit	structure_element	The extents of the 40S subunit rotation and head swivel relative to their positions in the post-translocation structure are shown with arrows.	FIG
44	48	head	structure_element	The extents of the 40S subunit rotation and head swivel relative to their positions in the post-translocation structure are shown with arrows.	FIG
91	109	post-translocation	protein_state	The extents of the 40S subunit rotation and head swivel relative to their positions in the post-translocation structure are shown with arrows.	FIG
110	119	structure	evidence	The extents of the 40S subunit rotation and head swivel relative to their positions in the post-translocation structure are shown with arrows.	FIG
13	20	cryo-EM	experimental_method	Schematic of cryo-EM refinement and classification procedures.	FIG
4	13	particles	experimental_method	All particles were initially aligned to a single model.	FIG
0	17	3D classification	experimental_method	3D classification using a 3D mask around the 40S head, TSV IRES and eEF2, of the 4x binned stack was used to identify particles containing both the IRES and eEF2.	FIG
26	33	3D mask	evidence	3D classification using a 3D mask around the 40S head, TSV IRES and eEF2, of the 4x binned stack was used to identify particles containing both the IRES and eEF2.	FIG
45	48	40S	complex_assembly	3D classification using a 3D mask around the 40S head, TSV IRES and eEF2, of the 4x binned stack was used to identify particles containing both the IRES and eEF2.	FIG
49	53	head	structure_element	3D classification using a 3D mask around the 40S head, TSV IRES and eEF2, of the 4x binned stack was used to identify particles containing both the IRES and eEF2.	FIG
55	58	TSV	species	3D classification using a 3D mask around the 40S head, TSV IRES and eEF2, of the 4x binned stack was used to identify particles containing both the IRES and eEF2.	FIG
59	63	IRES	site	3D classification using a 3D mask around the 40S head, TSV IRES and eEF2, of the 4x binned stack was used to identify particles containing both the IRES and eEF2.	FIG
68	72	eEF2	protein	3D classification using a 3D mask around the 40S head, TSV IRES and eEF2, of the 4x binned stack was used to identify particles containing both the IRES and eEF2.	FIG
91	96	stack	bond_interaction	3D classification using a 3D mask around the 40S head, TSV IRES and eEF2, of the 4x binned stack was used to identify particles containing both the IRES and eEF2.	FIG
118	127	particles	experimental_method	3D classification using a 3D mask around the 40S head, TSV IRES and eEF2, of the 4x binned stack was used to identify particles containing both the IRES and eEF2.	FIG
148	152	IRES	site	3D classification using a 3D mask around the 40S head, TSV IRES and eEF2, of the 4x binned stack was used to identify particles containing both the IRES and eEF2.	FIG
157	161	eEF2	protein	3D classification using a 3D mask around the 40S head, TSV IRES and eEF2, of the 4x binned stack was used to identify particles containing both the IRES and eEF2.	FIG
11	28	3D classification	experimental_method	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
37	44	2D mask	evidence	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
56	59	PKI	structure_element	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
71	73	IV	structure_element	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
77	81	eEF2	protein	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
124	146	Structures I through V	evidence	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
148	166	Sub-classification	experimental_method	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
234	241	density	evidence	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
249	252	PKI	structure_element	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
313	322	particles	experimental_method	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
330	344	sub-classified	experimental_method	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
345	359	reconstruction	evidence	Subsequent 3D classification using a 2D mask comprising PKI and domain IV of eEF2 yielded 5 'purified' classes representing Structures I through V. Sub-classification of each class did not yield additional classes, but helped improve density in the PKI region of class III (estimated resolution and percentage of particles in the sub-classified reconstruction are shown in parentheses).	FIG
0	7	Cryo-EM	experimental_method	Cryo-EM density of Structures I-V.	FIG
8	15	density	evidence	Cryo-EM density of Structures I-V.	FIG
19	33	Structures I-V	evidence	Cryo-EM density of Structures I-V.	FIG
21	25	maps	evidence	In panels (a-e), the maps are segmented and colored as in Figure 1.	FIG
4	8	maps	evidence	The maps in all panels were B-softened by applying a B-factor of 30 Å2.	FIG
6	13	Cryo-EM	experimental_method	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
14	17	map	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
21	52	Structures I, II, III, IV and V	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
104	111	cryo-EM	experimental_method	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
112	127	reconstructions	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
144	151	Blocres	experimental_method	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
180	211	Structures I, II, III, IV and V	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
219	226	Cryo-EM	experimental_method	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
227	234	density	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
243	246	TSV	species	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
247	251	IRES	site	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
268	272	eEF2	protein	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
290	321	Structures I, II, III, IV and V	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
327	352	Fourier shell correlation	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
354	357	FSC	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
359	365	curves	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
370	384	Structures I-V	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
508	511	FSC	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
570	578	FREALIGN	experimental_method	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
587	590	FSC	evidence	(a-e) Cryo-EM map of Structures I, II, III, IV and V. (f-j) Local resolution of unfiltered and unmasked cryo-EM reconstructions, assessed using Blocres from the BSoft package, for Structures I, II, III, IV and V. (k-o) Cryo-EM density for the TSV IRES (red model) and eEF2 (green model) in Structures I, II, III, IV and V. (p) Fourier shell correlation (FSC) curves for Structures I-V. The horizontal axis is labeled with spatial frequency Å-1 and with Å. The resolutions stated in the text correspond to an FSC threshold value of 0.143, shown as a dotted line, for the FREALIGN-derived FSC ('Part_FSC').	FIG
0	7	Cryo-EM	experimental_method	Cryo-EM structures of the 80S•TSV IRES bound with eEF2•GDP•sordarin.	FIG
8	18	structures	evidence	Cryo-EM structures of the 80S•TSV IRES bound with eEF2•GDP•sordarin.	FIG
26	38	80S•TSV IRES	complex_assembly	Cryo-EM structures of the 80S•TSV IRES bound with eEF2•GDP•sordarin.	FIG
39	49	bound with	protein_state	Cryo-EM structures of the 80S•TSV IRES bound with eEF2•GDP•sordarin.	FIG
50	67	eEF2•GDP•sordarin	complex_assembly	Cryo-EM structures of the 80S•TSV IRES bound with eEF2•GDP•sordarin.	FIG
4	26	Structures I through V	evidence	(a) Structures I through V. In all panels, the large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
47	70	large ribosomal subunit	structure_element	(a) Structures I through V. In all panels, the large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
93	106	small subunit	structure_element	(a) Structures I through V. In all panels, the large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
124	128	head	structure_element	(a) Structures I through V. In all panels, the large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
148	152	body	structure_element	(a) Structures I through V. In all panels, the large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
159	162	TSV	species	(a) Structures I through V. In all panels, the large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
163	167	IRES	site	(a) Structures I through V. In all panels, the large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
176	180	eEF2	protein	(a) Structures I through V. In all panels, the large ribosomal subunit is shown in cyan; the small subunit in light yellow (head) and wheat-yellow (body); the TSV IRES in red, eEF2 in green.	FIG
12	17	C1274	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
19	24	U1191	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
32	35	40S	complex_assembly	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
36	40	head	structure_element	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
45	49	G904	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
57	65	platform	site	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
67	72	C1054	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
74	78	G966	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
83	87	G693	residue_name_number	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
91	98	E. coli	species	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
99	107	16S rRNA	chemical	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
142	158	A, P and E sites	site	Nucleotides C1274, U1191 of the 40S head and G904 of the platform (C1054, G966 and G693 in E. coli 16S rRNA) are shown in black to denote the A, P and E sites, respectively.	FIG
36	46	structures	evidence	(b) Schematic representation of the structures shown in panel a, denoting the conformations of the small subunit relative to the large subunit.	FIG
99	112	small subunit	structure_element	(b) Schematic representation of the structures shown in panel a, denoting the conformations of the small subunit relative to the large subunit.	FIG
129	142	large subunit	structure_element	(b) Schematic representation of the structures shown in panel a, denoting the conformations of the small subunit relative to the large subunit.	FIG
0	16	A, P and E sites	site	A, P and E sites are shown as rectangles.	FIG
37	48	non-rotated	protein_state	All measurements are relative to the non-rotated 80S•2tRNA•mRNA structure.	FIG
49	63	80S•2tRNA•mRNA	complex_assembly	All measurements are relative to the non-rotated 80S•2tRNA•mRNA structure.	FIG
64	73	structure	evidence	All measurements are relative to the non-rotated 80S•2tRNA•mRNA structure.	FIG
37	48	non-rotated	protein_state	All measurements are relative to the non-rotated 80S•2tRNA•mRNA structure.	FIG
49	63	80S•2tRNA•mRNA	complex_assembly	All measurements are relative to the non-rotated 80S•2tRNA•mRNA structure.	FIG
64	73	structure	evidence	All measurements are relative to the non-rotated 80S•2tRNA•mRNA structure.	FIG
48	72	structural visualization	experimental_method	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
76	89	80S•IRES•eEF2	complex_assembly	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
136	140	IRES	site	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
141	144	RNA	chemical	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
202	205	PKI	structure_element	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
215	226	A to P site	site	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
234	247	small subunit	structure_element	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
262	266	eEF2	protein	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
275	279	IRES	site	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
304	308	IRES	site	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
359	367	ribosome	complex_assembly	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
380	384	tRNA	chemical	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
445	448	40S	complex_assembly	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
449	453	head	structure_element	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
466	470	IRES	site	We sought to address the following questions by structural visualization of 80S•IRES•eEF2 translocation complexes: (1) How does a large IRES RNA move through the restricted intersubunit space, bringing PKI from the A to P site of the small subunit? (2) How does eEF2 mediate IRES translocation? (3) Does IRES translocation involve large rearrangements in the ribosome, similar to tRNA translocation? (4) What, if any, is the mechanistic role of 40S head rotation in IRES translocation?	INTRO
8	15	cryo-EM	experimental_method	We used cryo-EM to visualize 80S•TSV IRES complexes formed in the presence of eEF2•GTP and the translation inhibitor sordarin, which stabilizes eEF2 on the ribosome.	INTRO
29	41	80S•TSV IRES	complex_assembly	We used cryo-EM to visualize 80S•TSV IRES complexes formed in the presence of eEF2•GTP and the translation inhibitor sordarin, which stabilizes eEF2 on the ribosome.	INTRO
66	77	presence of	protein_state	We used cryo-EM to visualize 80S•TSV IRES complexes formed in the presence of eEF2•GTP and the translation inhibitor sordarin, which stabilizes eEF2 on the ribosome.	INTRO
78	86	eEF2•GTP	complex_assembly	We used cryo-EM to visualize 80S•TSV IRES complexes formed in the presence of eEF2•GTP and the translation inhibitor sordarin, which stabilizes eEF2 on the ribosome.	INTRO
117	125	sordarin	chemical	We used cryo-EM to visualize 80S•TSV IRES complexes formed in the presence of eEF2•GTP and the translation inhibitor sordarin, which stabilizes eEF2 on the ribosome.	INTRO
144	148	eEF2	protein	We used cryo-EM to visualize 80S•TSV IRES complexes formed in the presence of eEF2•GTP and the translation inhibitor sordarin, which stabilizes eEF2 on the ribosome.	INTRO
156	164	ribosome	complex_assembly	We used cryo-EM to visualize 80S•TSV IRES complexes formed in the presence of eEF2•GTP and the translation inhibitor sordarin, which stabilizes eEF2 on the ribosome.	INTRO
26	34	sordarin	chemical	Although the mechanism of sordarin action is not fully understood, the inhibitor does not affect the conformation of eEF2•GDPNP on the ribosome, rendering it an excellent tool in translocation studies.	INTRO
117	127	eEF2•GDPNP	complex_assembly	Although the mechanism of sordarin action is not fully understood, the inhibitor does not affect the conformation of eEF2•GDPNP on the ribosome, rendering it an excellent tool in translocation studies.	INTRO
135	143	ribosome	complex_assembly	Although the mechanism of sordarin action is not fully understood, the inhibitor does not affect the conformation of eEF2•GDPNP on the ribosome, rendering it an excellent tool in translocation studies.	INTRO
0	33	Maximum-likelihood classification	experimental_method	Maximum-likelihood classification using FREALIGN identified five IRES-eEF2-bound ribosome structures within a single sample (Figures 1 and 2).	INTRO
40	48	FREALIGN	experimental_method	Maximum-likelihood classification using FREALIGN identified five IRES-eEF2-bound ribosome structures within a single sample (Figures 1 and 2).	INTRO
65	80	IRES-eEF2-bound	protein_state	Maximum-likelihood classification using FREALIGN identified five IRES-eEF2-bound ribosome structures within a single sample (Figures 1 and 2).	INTRO
81	89	ribosome	complex_assembly	Maximum-likelihood classification using FREALIGN identified five IRES-eEF2-bound ribosome structures within a single sample (Figures 1 and 2).	INTRO
90	100	structures	evidence	Maximum-likelihood classification using FREALIGN identified five IRES-eEF2-bound ribosome structures within a single sample (Figures 1 and 2).	INTRO
4	14	structures	evidence	The structures differ in the positions and conformations of ribosomal subunits (Figures 1b and 2), IRES RNA (Figures 3 and 4) and eEF2 (Figures 5 and 6).	INTRO
99	103	IRES	site	The structures differ in the positions and conformations of ribosomal subunits (Figures 1b and 2), IRES RNA (Figures 3 and 4) and eEF2 (Figures 5 and 6).	INTRO
104	107	RNA	chemical	The structures differ in the positions and conformations of ribosomal subunits (Figures 1b and 2), IRES RNA (Figures 3 and 4) and eEF2 (Figures 5 and 6).	INTRO
130	134	eEF2	protein	The structures differ in the positions and conformations of ribosomal subunits (Figures 1b and 2), IRES RNA (Figures 3 and 4) and eEF2 (Figures 5 and 6).	INTRO
17	27	structures	evidence	This ensemble of structures allowed us to reconstruct a sequence of steps in IRES translocation induced by eEF2.	INTRO
77	81	IRES	site	This ensemble of structures allowed us to reconstruct a sequence of steps in IRES translocation induced by eEF2.	INTRO
107	111	eEF2	protein	This ensemble of structures allowed us to reconstruct a sequence of steps in IRES translocation induced by eEF2.	INTRO
8	31	single-particle cryo-EM	experimental_method	We used single-particle cryo-EM and maximum-likelihood image classification in FREALIGN to obtain three-dimensional density maps from a single specimen.	RESULTS
36	75	maximum-likelihood image classification	experimental_method	We used single-particle cryo-EM and maximum-likelihood image classification in FREALIGN to obtain three-dimensional density maps from a single specimen.	RESULTS
79	87	FREALIGN	experimental_method	We used single-particle cryo-EM and maximum-likelihood image classification in FREALIGN to obtain three-dimensional density maps from a single specimen.	RESULTS
116	128	density maps	evidence	We used single-particle cryo-EM and maximum-likelihood image classification in FREALIGN to obtain three-dimensional density maps from a single specimen.	RESULTS
43	56	S. cerevisiae	species	The translocation complex was formed using S. cerevisiae 80S ribosomes, Taura syndrome virus IRES, and S. cerevisiae eEF2 in the presence of GTP and the eEF2-binding translation inhibitor sordarin.	RESULTS
57	70	80S ribosomes	complex_assembly	The translocation complex was formed using S. cerevisiae 80S ribosomes, Taura syndrome virus IRES, and S. cerevisiae eEF2 in the presence of GTP and the eEF2-binding translation inhibitor sordarin.	RESULTS
72	92	Taura syndrome virus	species	The translocation complex was formed using S. cerevisiae 80S ribosomes, Taura syndrome virus IRES, and S. cerevisiae eEF2 in the presence of GTP and the eEF2-binding translation inhibitor sordarin.	RESULTS
93	97	IRES	site	The translocation complex was formed using S. cerevisiae 80S ribosomes, Taura syndrome virus IRES, and S. cerevisiae eEF2 in the presence of GTP and the eEF2-binding translation inhibitor sordarin.	RESULTS
103	116	S. cerevisiae	species	The translocation complex was formed using S. cerevisiae 80S ribosomes, Taura syndrome virus IRES, and S. cerevisiae eEF2 in the presence of GTP and the eEF2-binding translation inhibitor sordarin.	RESULTS
117	121	eEF2	protein	The translocation complex was formed using S. cerevisiae 80S ribosomes, Taura syndrome virus IRES, and S. cerevisiae eEF2 in the presence of GTP and the eEF2-binding translation inhibitor sordarin.	RESULTS
129	140	presence of	protein_state	The translocation complex was formed using S. cerevisiae 80S ribosomes, Taura syndrome virus IRES, and S. cerevisiae eEF2 in the presence of GTP and the eEF2-binding translation inhibitor sordarin.	RESULTS
141	144	GTP	chemical	The translocation complex was formed using S. cerevisiae 80S ribosomes, Taura syndrome virus IRES, and S. cerevisiae eEF2 in the presence of GTP and the eEF2-binding translation inhibitor sordarin.	RESULTS
153	157	eEF2	protein	The translocation complex was formed using S. cerevisiae 80S ribosomes, Taura syndrome virus IRES, and S. cerevisiae eEF2 in the presence of GTP and the eEF2-binding translation inhibitor sordarin.	RESULTS
188	196	sordarin	chemical	The translocation complex was formed using S. cerevisiae 80S ribosomes, Taura syndrome virus IRES, and S. cerevisiae eEF2 in the presence of GTP and the eEF2-binding translation inhibitor sordarin.	RESULTS
0	40	Unsupervised cryo-EM data classification	experimental_method	Unsupervised cryo-EM data classification was combined with the use of three-dimensional and two-dimensional masking around the ribosomal A site (Figure 1—figure supplement 2).	RESULTS
70	115	three-dimensional and two-dimensional masking	experimental_method	Unsupervised cryo-EM data classification was combined with the use of three-dimensional and two-dimensional masking around the ribosomal A site (Figure 1—figure supplement 2).	RESULTS
137	143	A site	site	Unsupervised cryo-EM data classification was combined with the use of three-dimensional and two-dimensional masking around the ribosomal A site (Figure 1—figure supplement 2).	RESULTS
28	45	80S•IRES•eEF2•GDP	complex_assembly	This approach revealed five 80S•IRES•eEF2•GDP structures at average resolutions of 3.5 to 4.2 Å, sufficient to locate IRES domains and to resolve individual residues in the core regions of the ribosome and eEF2 (Figures 3c,d, and 5f,h; see also Figure 1—figure supplement 2 and Figure 5—figure supplement 2), including the post-translational modification diphthamide 699 (Figure 3c).	RESULTS
46	56	structures	evidence	This approach revealed five 80S•IRES•eEF2•GDP structures at average resolutions of 3.5 to 4.2 Å, sufficient to locate IRES domains and to resolve individual residues in the core regions of the ribosome and eEF2 (Figures 3c,d, and 5f,h; see also Figure 1—figure supplement 2 and Figure 5—figure supplement 2), including the post-translational modification diphthamide 699 (Figure 3c).	RESULTS
118	122	IRES	site	This approach revealed five 80S•IRES•eEF2•GDP structures at average resolutions of 3.5 to 4.2 Å, sufficient to locate IRES domains and to resolve individual residues in the core regions of the ribosome and eEF2 (Figures 3c,d, and 5f,h; see also Figure 1—figure supplement 2 and Figure 5—figure supplement 2), including the post-translational modification diphthamide 699 (Figure 3c).	RESULTS
193	201	ribosome	complex_assembly	This approach revealed five 80S•IRES•eEF2•GDP structures at average resolutions of 3.5 to 4.2 Å, sufficient to locate IRES domains and to resolve individual residues in the core regions of the ribosome and eEF2 (Figures 3c,d, and 5f,h; see also Figure 1—figure supplement 2 and Figure 5—figure supplement 2), including the post-translational modification diphthamide 699 (Figure 3c).	RESULTS
206	210	eEF2	protein	This approach revealed five 80S•IRES•eEF2•GDP structures at average resolutions of 3.5 to 4.2 Å, sufficient to locate IRES domains and to resolve individual residues in the core regions of the ribosome and eEF2 (Figures 3c,d, and 5f,h; see also Figure 1—figure supplement 2 and Figure 5—figure supplement 2), including the post-translational modification diphthamide 699 (Figure 3c).	RESULTS
355	370	diphthamide 699	ptm	This approach revealed five 80S•IRES•eEF2•GDP structures at average resolutions of 3.5 to 4.2 Å, sufficient to locate IRES domains and to resolve individual residues in the core regions of the ribosome and eEF2 (Figures 3c,d, and 5f,h; see also Figure 1—figure supplement 2 and Figure 5—figure supplement 2), including the post-translational modification diphthamide 699 (Figure 3c).	RESULTS
30	52	Structures I through V	evidence	Large-scale rearrangements in Structures I through V, coupled with the movement of PKI from the A to P site and eEF2 entry into the A site.	FIG
83	86	PKI	structure_element	Large-scale rearrangements in Structures I through V, coupled with the movement of PKI from the A to P site and eEF2 entry into the A site.	FIG
96	107	A to P site	site	Large-scale rearrangements in Structures I through V, coupled with the movement of PKI from the A to P site and eEF2 entry into the A site.	FIG
112	116	eEF2	protein	Large-scale rearrangements in Structures I through V, coupled with the movement of PKI from the A to P site and eEF2 entry into the A site.	FIG
132	138	A site	site	Large-scale rearrangements in Structures I through V, coupled with the movement of PKI from the A to P site and eEF2 entry into the A site.	FIG
30	52	Structures I through V	evidence	Large-scale rearrangements in Structures I through V, coupled with the movement of PKI from the A to P site and eEF2 entry into the A site.	FIG
83	86	PKI	structure_element	Large-scale rearrangements in Structures I through V, coupled with the movement of PKI from the A to P site and eEF2 entry into the A site.	FIG
96	107	A to P site	site	Large-scale rearrangements in Structures I through V, coupled with the movement of PKI from the A to P site and eEF2 entry into the A site.	FIG
112	116	eEF2	protein	Large-scale rearrangements in Structures I through V, coupled with the movement of PKI from the A to P site and eEF2 entry into the A site.	FIG
132	138	A site	site	Large-scale rearrangements in Structures I through V, coupled with the movement of PKI from the A to P site and eEF2 entry into the A site.	FIG
29	32	40S	complex_assembly	(a) Rotational states of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
33	40	subunit	structure_element	(a) Rotational states of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
48	56	80S•IRES	complex_assembly	(a) Rotational states of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
57	66	structure	evidence	(a) Rotational states of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
68	72	INIT	complex_assembly	(a) Rotational states of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
91	104	80S•IRES•eEF2	complex_assembly	(a) Rotational states of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
105	136	Structures I, II, III, IV and V	evidence	(a) Rotational states of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
9	18	structure	evidence	For each structure, the triangle outlines the contours of the 40S body; the lower angle illustrates the extent of intersubunit (body) rotation.	FIG
62	65	40S	complex_assembly	For each structure, the triangle outlines the contours of the 40S body; the lower angle illustrates the extent of intersubunit (body) rotation.	FIG
66	70	body	structure_element	For each structure, the triangle outlines the contours of the 40S body; the lower angle illustrates the extent of intersubunit (body) rotation.	FIG
128	132	body	structure_element	For each structure, the triangle outlines the contours of the 40S body; the lower angle illustrates the extent of intersubunit (body) rotation.	FIG
56	60	head	structure_element	The sizes of the arrows correspond to the extent of the head swivel (yellow) and subunit rotation (black).	FIG
81	88	subunit	structure_element	The sizes of the arrows correspond to the extent of the head swivel (yellow) and subunit rotation (black).	FIG
27	47	structural alignment	experimental_method	The views were obtained by structural alignment of the 25S rRNAs; the sarcin-ricin loop (SRL) of 25S rRNA is shown in gray for reference.	FIG
55	64	25S rRNAs	chemical	The views were obtained by structural alignment of the 25S rRNAs; the sarcin-ricin loop (SRL) of 25S rRNA is shown in gray for reference.	FIG
70	87	sarcin-ricin loop	structure_element	The views were obtained by structural alignment of the 25S rRNAs; the sarcin-ricin loop (SRL) of 25S rRNA is shown in gray for reference.	FIG
89	92	SRL	structure_element	The views were obtained by structural alignment of the 25S rRNAs; the sarcin-ricin loop (SRL) of 25S rRNA is shown in gray for reference.	FIG
97	105	25S rRNA	chemical	The views were obtained by structural alignment of the 25S rRNAs; the sarcin-ricin loop (SRL) of 25S rRNA is shown in gray for reference.	FIG
58	61	40S	complex_assembly	(b) Solvent view (opposite from that shown in (a)) of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
62	69	subunit	structure_element	(b) Solvent view (opposite from that shown in (a)) of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
77	85	80S•IRES	complex_assembly	(b) Solvent view (opposite from that shown in (a)) of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
86	95	structure	evidence	(b) Solvent view (opposite from that shown in (a)) of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
97	101	INIT	complex_assembly	(b) Solvent view (opposite from that shown in (a)) of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
120	133	80S•IRES•eEF2	complex_assembly	(b) Solvent view (opposite from that shown in (a)) of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
134	165	Structures I, II, III, IV and V	evidence	(b) Solvent view (opposite from that shown in (a)) of the 40S subunit in the 80S•IRES structure (INIT; PDB 3J6Y) and in 80S•IRES•eEF2 Structures I, II, III, IV and V (this work).	FIG
4	14	structures	evidence	The structures are colored as in Figure 1.	FIG
22	25	40S	complex_assembly	(a) Comparison of the 40S-subunit rotational states in Structures I through V, sampling a ~10° range between Structure I (fully rotated) and Structure V (non-rotated).	FIG
26	33	subunit	structure_element	(a) Comparison of the 40S-subunit rotational states in Structures I through V, sampling a ~10° range between Structure I (fully rotated) and Structure V (non-rotated).	FIG
55	77	Structures I through V	evidence	(a) Comparison of the 40S-subunit rotational states in Structures I through V, sampling a ~10° range between Structure I (fully rotated) and Structure V (non-rotated).	FIG
109	120	Structure I	evidence	(a) Comparison of the 40S-subunit rotational states in Structures I through V, sampling a ~10° range between Structure I (fully rotated) and Structure V (non-rotated).	FIG
122	135	fully rotated	protein_state	(a) Comparison of the 40S-subunit rotational states in Structures I through V, sampling a ~10° range between Structure I (fully rotated) and Structure V (non-rotated).	FIG
141	152	Structure V	evidence	(a) Comparison of the 40S-subunit rotational states in Structures I through V, sampling a ~10° range between Structure I (fully rotated) and Structure V (non-rotated).	FIG
154	165	non-rotated	protein_state	(a) Comparison of the 40S-subunit rotational states in Structures I through V, sampling a ~10° range between Structure I (fully rotated) and Structure V (non-rotated).	FIG
0	17	18S ribosomal RNA	chemical	18S ribosomal RNA is shown and ribosomal proteins are omitted for clarity.	FIG
4	18	superpositions	experimental_method	The superpositions of Structures I-V were performed by structural alignments of the 25S ribosomal RNAs.	FIG
22	36	Structures I-V	evidence	The superpositions of Structures I-V were performed by structural alignments of the 25S ribosomal RNAs.	FIG
55	76	structural alignments	experimental_method	The superpositions of Structures I-V were performed by structural alignments of the 25S ribosomal RNAs.	FIG
84	102	25S ribosomal RNAs	chemical	The superpositions of Structures I-V were performed by structural alignments of the 25S ribosomal RNAs.	FIG
47	50	40S	complex_assembly	(b) Bar graph of the angles characterizing the 40S rotational and 40S head swiveling states in Structures I through V. Measurements for the two 80S•IRES (INIT) structures are included for comparison.	FIG
66	69	40S	complex_assembly	(b) Bar graph of the angles characterizing the 40S rotational and 40S head swiveling states in Structures I through V. Measurements for the two 80S•IRES (INIT) structures are included for comparison.	FIG
70	74	head	structure_element	(b) Bar graph of the angles characterizing the 40S rotational and 40S head swiveling states in Structures I through V. Measurements for the two 80S•IRES (INIT) structures are included for comparison.	FIG
95	117	Structures I through V	evidence	(b) Bar graph of the angles characterizing the 40S rotational and 40S head swiveling states in Structures I through V. Measurements for the two 80S•IRES (INIT) structures are included for comparison.	FIG
144	152	80S•IRES	complex_assembly	(b) Bar graph of the angles characterizing the 40S rotational and 40S head swiveling states in Structures I through V. Measurements for the two 80S•IRES (INIT) structures are included for comparison.	FIG
154	158	INIT	complex_assembly	(b) Bar graph of the angles characterizing the 40S rotational and 40S head swiveling states in Structures I through V. Measurements for the two 80S•IRES (INIT) structures are included for comparison.	FIG
160	170	structures	evidence	(b) Bar graph of the angles characterizing the 40S rotational and 40S head swiveling states in Structures I through V. Measurements for the two 80S•IRES (INIT) structures are included for comparison.	FIG
22	25	40S	complex_assembly	(c) Comparison of the 40S conformations in Structures I through V shows distinct positions of the head relative to the body of the 40S subunit (head swivel).	FIG
43	65	Structures I through V	evidence	(c) Comparison of the 40S conformations in Structures I through V shows distinct positions of the head relative to the body of the 40S subunit (head swivel).	FIG
98	102	head	structure_element	(c) Comparison of the 40S conformations in Structures I through V shows distinct positions of the head relative to the body of the 40S subunit (head swivel).	FIG
119	123	body	structure_element	(c) Comparison of the 40S conformations in Structures I through V shows distinct positions of the head relative to the body of the 40S subunit (head swivel).	FIG
131	134	40S	complex_assembly	(c) Comparison of the 40S conformations in Structures I through V shows distinct positions of the head relative to the body of the 40S subunit (head swivel).	FIG
135	142	subunit	structure_element	(c) Comparison of the 40S conformations in Structures I through V shows distinct positions of the head relative to the body of the 40S subunit (head swivel).	FIG
144	148	head	structure_element	(c) Comparison of the 40S conformations in Structures I through V shows distinct positions of the head relative to the body of the 40S subunit (head swivel).	FIG
20	32	non-swiveled	protein_state	Conformation of the non-swiveled 40S subunit in the S. cerevisiae 80S ribosome bound with two tRNAs is shown for reference (blue).	FIG
33	36	40S	complex_assembly	Conformation of the non-swiveled 40S subunit in the S. cerevisiae 80S ribosome bound with two tRNAs is shown for reference (blue).	FIG
37	44	subunit	structure_element	Conformation of the non-swiveled 40S subunit in the S. cerevisiae 80S ribosome bound with two tRNAs is shown for reference (blue).	FIG
52	65	S. cerevisiae	species	Conformation of the non-swiveled 40S subunit in the S. cerevisiae 80S ribosome bound with two tRNAs is shown for reference (blue).	FIG
66	78	80S ribosome	complex_assembly	Conformation of the non-swiveled 40S subunit in the S. cerevisiae 80S ribosome bound with two tRNAs is shown for reference (blue).	FIG
79	89	bound with	protein_state	Conformation of the non-swiveled 40S subunit in the S. cerevisiae 80S ribosome bound with two tRNAs is shown for reference (blue).	FIG
94	99	tRNAs	chemical	Conformation of the non-swiveled 40S subunit in the S. cerevisiae 80S ribosome bound with two tRNAs is shown for reference (blue).	FIG
39	41	L1	structure_element	(d) Comparison of conformations of the L1 and P stalks of the large subunit in Structures I through V with those in the 80S•IRES and tRNA-bound 80S structures.	FIG
46	54	P stalks	structure_element	(d) Comparison of conformations of the L1 and P stalks of the large subunit in Structures I through V with those in the 80S•IRES and tRNA-bound 80S structures.	FIG
62	75	large subunit	structure_element	(d) Comparison of conformations of the L1 and P stalks of the large subunit in Structures I through V with those in the 80S•IRES and tRNA-bound 80S structures.	FIG
79	101	Structures I through V	evidence	(d) Comparison of conformations of the L1 and P stalks of the large subunit in Structures I through V with those in the 80S•IRES and tRNA-bound 80S structures.	FIG
120	128	80S•IRES	complex_assembly	(d) Comparison of conformations of the L1 and P stalks of the large subunit in Structures I through V with those in the 80S•IRES and tRNA-bound 80S structures.	FIG
133	143	tRNA-bound	protein_state	(d) Comparison of conformations of the L1 and P stalks of the large subunit in Structures I through V with those in the 80S•IRES and tRNA-bound 80S structures.	FIG
144	147	80S	complex_assembly	(d) Comparison of conformations of the L1 and P stalks of the large subunit in Structures I through V with those in the 80S•IRES and tRNA-bound 80S structures.	FIG
148	158	structures	evidence	(d) Comparison of conformations of the L1 and P stalks of the large subunit in Structures I through V with those in the 80S•IRES and tRNA-bound 80S structures.	FIG
0	14	Superpositions	experimental_method	Superpositions were performed by structural alignments of 25S ribosomal RNAs.	FIG
33	54	structural alignments	experimental_method	Superpositions were performed by structural alignments of 25S ribosomal RNAs.	FIG
58	76	25S ribosomal RNAs	chemical	Superpositions were performed by structural alignments of 25S ribosomal RNAs.	FIG
4	24	central protuberance	structure_element	The central protuberance (CP) is labeled.	FIG
26	28	CP	structure_element	The central protuberance (CP) is labeled.	FIG
35	38	PKI	structure_element	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
50	52	IV	structure_element	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
56	60	eEF2	protein	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
77	83	P site	site	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
100	104	head	structure_element	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
106	111	U1191	residue_name_number	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
117	121	body	structure_element	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
123	128	C1637	residue_name_number	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
133	155	Structures I through V	evidence	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
206	219	A and P sites	site	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
229	239	initiation	protein_state	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
247	251	INIT	complex_assembly	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
273	291	post-translocation	protein_state	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
292	303	Structure V	evidence	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
398	401	40S	complex_assembly	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
402	406	body	structure_element	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
428	431	40S	complex_assembly	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
432	436	head	structure_element	 (e) Bar graph of the positions of PKI and domain IV of eEF2 relative to the P site residues of the head (U1191) and body (C1637) in Structures I through V. (f and g) Close-up view of rearrangements in the A and P sites from the initiation state (INIT: PDB ID 3J6Y) to the post-translocation Structure V. The fragment shown within a rectangle in panel f is magnified in panel g. Nucleotides of the 40S body are shown in orange, 40S head in yellow.	FIG
4	18	superpositions	experimental_method	The superpositions of structures were performed by structural alignments of the 18S ribosomal RNAs excluding the head region (nt 1150–1620).	FIG
22	32	structures	evidence	The superpositions of structures were performed by structural alignments of the 18S ribosomal RNAs excluding the head region (nt 1150–1620).	FIG
51	72	structural alignments	experimental_method	The superpositions of structures were performed by structural alignments of the 18S ribosomal RNAs excluding the head region (nt 1150–1620).	FIG
80	98	18S ribosomal RNAs	chemical	The superpositions of structures were performed by structural alignments of the 18S ribosomal RNAs excluding the head region (nt 1150–1620).	FIG
113	117	head	structure_element	The superpositions of structures were performed by structural alignments of the 18S ribosomal RNAs excluding the head region (nt 1150–1620).	FIG
129	138	1150–1620	residue_range	The superpositions of structures were performed by structural alignments of the 18S ribosomal RNAs excluding the head region (nt 1150–1620).	FIG
4	14	structures	evidence	Our structures represent hitherto uncharacterized translocation complexes of the TSV IRES captured within globally distinct 80S conformations (Figures 1b and 2).	RESULTS
81	84	TSV	species	Our structures represent hitherto uncharacterized translocation complexes of the TSV IRES captured within globally distinct 80S conformations (Figures 1b and 2).	RESULTS
85	89	IRES	site	Our structures represent hitherto uncharacterized translocation complexes of the TSV IRES captured within globally distinct 80S conformations (Figures 1b and 2).	RESULTS
124	127	80S	complex_assembly	Our structures represent hitherto uncharacterized translocation complexes of the TSV IRES captured within globally distinct 80S conformations (Figures 1b and 2).	RESULTS
16	38	structures from I to V	evidence	We numbered the structures from I to V, according to the position of the tRNA-mRNA-like PKI on the 40S subunit (Figure 2—source data 1).	RESULTS
73	82	tRNA-mRNA	complex_assembly	We numbered the structures from I to V, according to the position of the tRNA-mRNA-like PKI on the 40S subunit (Figure 2—source data 1).	RESULTS
88	91	PKI	structure_element	We numbered the structures from I to V, according to the position of the tRNA-mRNA-like PKI on the 40S subunit (Figure 2—source data 1).	RESULTS
99	102	40S	complex_assembly	We numbered the structures from I to V, according to the position of the tRNA-mRNA-like PKI on the 40S subunit (Figure 2—source data 1).	RESULTS
103	110	subunit	structure_element	We numbered the structures from I to V, according to the position of the tRNA-mRNA-like PKI on the 40S subunit (Figure 2—source data 1).	RESULTS
14	17	PKI	structure_element	Specifically, PKI is partially withdrawn from the A site in Structure I, and fully translocated to the P site in Structure V (Figure 4; see also Figure 3—figure supplement 1).	RESULTS
50	56	A site	site	Specifically, PKI is partially withdrawn from the A site in Structure I, and fully translocated to the P site in Structure V (Figure 4; see also Figure 3—figure supplement 1).	RESULTS
60	71	Structure I	evidence	Specifically, PKI is partially withdrawn from the A site in Structure I, and fully translocated to the P site in Structure V (Figure 4; see also Figure 3—figure supplement 1).	RESULTS
77	95	fully translocated	protein_state	Specifically, PKI is partially withdrawn from the A site in Structure I, and fully translocated to the P site in Structure V (Figure 4; see also Figure 3—figure supplement 1).	RESULTS
103	109	P site	site	Specifically, PKI is partially withdrawn from the A site in Structure I, and fully translocated to the P site in Structure V (Figure 4; see also Figure 3—figure supplement 1).	RESULTS
113	124	Structure V	evidence	Specifically, PKI is partially withdrawn from the A site in Structure I, and fully translocated to the P site in Structure V (Figure 4; see also Figure 3—figure supplement 1).	RESULTS
5	23	Structures I to IV	evidence	Thus Structures I to IV represent different positions of PKI between the A and P sites (Figure 2—source data 1), suggesting that these structures describe intermediate states of translocation.	RESULTS
57	60	PKI	structure_element	Thus Structures I to IV represent different positions of PKI between the A and P sites (Figure 2—source data 1), suggesting that these structures describe intermediate states of translocation.	RESULTS
73	86	A and P sites	site	Thus Structures I to IV represent different positions of PKI between the A and P sites (Figure 2—source data 1), suggesting that these structures describe intermediate states of translocation.	RESULTS
135	145	structures	evidence	Thus Structures I to IV represent different positions of PKI between the A and P sites (Figure 2—source data 1), suggesting that these structures describe intermediate states of translocation.	RESULTS
0	11	Structure V	evidence	Structure V corresponds to the post-translocation state.	RESULTS
31	49	post-translocation	protein_state	Structure V corresponds to the post-translocation state.	RESULTS
11	19	ribosome	complex_assembly	Changes in ribosome conformation and eEF2 positions are coupled with IRES movement through the ribosome	RESULTS
37	41	eEF2	protein	Changes in ribosome conformation and eEF2 positions are coupled with IRES movement through the ribosome	RESULTS
69	73	IRES	site	Changes in ribosome conformation and eEF2 positions are coupled with IRES movement through the ribosome	RESULTS
95	103	ribosome	complex_assembly	Changes in ribosome conformation and eEF2 positions are coupled with IRES movement through the ribosome	RESULTS
10	28	post-translocation	protein_state	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
29	42	S. cerevisiae	species	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
43	55	80S ribosome	complex_assembly	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
56	66	bound with	protein_state	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
71	83	P and E site	site	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
84	89	tRNAs	chemical	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
106	120	80S•2tRNA•mRNA	complex_assembly	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
141	148	subunit	structure_element	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
166	170	head	structure_element	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
171	175	body	structure_element	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
209	217	ribosome	complex_assembly	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
265	287	Structures I through V	evidence	Using the post-translocation S. cerevisiae 80S ribosome bound with the P and E site tRNAs as a reference (80S•2tRNA•mRNA), in which both the subunit rotation and the head-body swivel are 0°, we found that the ribosome adopts four globally distinct conformations in Structures I through V (Figure 1b; see also Figure 1—figure supplement 1 and Figure 2—source data 1).	RESULTS
0	11	Structure I	evidence	Structure I comprises the most rotated ribosome conformation (~10°), characteristic of pre-translocation hybrid-tRNA states.	RESULTS
26	38	most rotated	protein_state	Structure I comprises the most rotated ribosome conformation (~10°), characteristic of pre-translocation hybrid-tRNA states.	RESULTS
39	47	ribosome	complex_assembly	Structure I comprises the most rotated ribosome conformation (~10°), characteristic of pre-translocation hybrid-tRNA states.	RESULTS
87	104	pre-translocation	protein_state	Structure I comprises the most rotated ribosome conformation (~10°), characteristic of pre-translocation hybrid-tRNA states.	RESULTS
105	116	hybrid-tRNA	protein_state	Structure I comprises the most rotated ribosome conformation (~10°), characteristic of pre-translocation hybrid-tRNA states.	RESULTS
5	21	Structure I to V	evidence	From Structure I to V, the body of the small subunit undergoes backward (reverse) rotation (Figure 2b; see also Figure 1—figure supplement 2 and Figure 2—figure supplement 1).	RESULTS
27	31	body	structure_element	From Structure I to V, the body of the small subunit undergoes backward (reverse) rotation (Figure 2b; see also Figure 1—figure supplement 2 and Figure 2—figure supplement 1).	RESULTS
39	52	small subunit	structure_element	From Structure I to V, the body of the small subunit undergoes backward (reverse) rotation (Figure 2b; see also Figure 1—figure supplement 2 and Figure 2—figure supplement 1).	RESULTS
0	21	Structures II and III	evidence	Structures II and III are in mid-rotation conformations (~5°).	RESULTS
29	41	mid-rotation	protein_state	Structures II and III are in mid-rotation conformations (~5°).	RESULTS
0	12	Structure IV	evidence	Structure IV adopts a slightly rotated conformation (~1°).	RESULTS
22	38	slightly rotated	protein_state	Structure IV adopts a slightly rotated conformation (~1°).	RESULTS
0	11	Structure V	evidence	Structure V is in a nearly non-rotated conformation (0.5°), very similar to that of post-translocation ribosome-tRNA complexes.	RESULTS
27	38	non-rotated	protein_state	Structure V is in a nearly non-rotated conformation (0.5°), very similar to that of post-translocation ribosome-tRNA complexes.	RESULTS
84	102	post-translocation	protein_state	Structure V is in a nearly non-rotated conformation (0.5°), very similar to that of post-translocation ribosome-tRNA complexes.	RESULTS
103	116	ribosome-tRNA	complex_assembly	Structure V is in a nearly non-rotated conformation (0.5°), very similar to that of post-translocation ribosome-tRNA complexes.	RESULTS
40	56	Structure I to V	evidence	Thus, intersubunit rotation of ~9° from Structure I to V covers a nearly complete range of relative subunit positions, similar to what was reported for tRNA-bound yeast, bacterial and mammalian ribosomes.	RESULTS
100	107	subunit	structure_element	Thus, intersubunit rotation of ~9° from Structure I to V covers a nearly complete range of relative subunit positions, similar to what was reported for tRNA-bound yeast, bacterial and mammalian ribosomes.	RESULTS
152	162	tRNA-bound	protein_state	Thus, intersubunit rotation of ~9° from Structure I to V covers a nearly complete range of relative subunit positions, similar to what was reported for tRNA-bound yeast, bacterial and mammalian ribosomes.	RESULTS
163	168	yeast	taxonomy_domain	Thus, intersubunit rotation of ~9° from Structure I to V covers a nearly complete range of relative subunit positions, similar to what was reported for tRNA-bound yeast, bacterial and mammalian ribosomes.	RESULTS
170	179	bacterial	taxonomy_domain	Thus, intersubunit rotation of ~9° from Structure I to V covers a nearly complete range of relative subunit positions, similar to what was reported for tRNA-bound yeast, bacterial and mammalian ribosomes.	RESULTS
184	193	mammalian	taxonomy_domain	Thus, intersubunit rotation of ~9° from Structure I to V covers a nearly complete range of relative subunit positions, similar to what was reported for tRNA-bound yeast, bacterial and mammalian ribosomes.	RESULTS
194	203	ribosomes	complex_assembly	Thus, intersubunit rotation of ~9° from Structure I to V covers a nearly complete range of relative subunit positions, similar to what was reported for tRNA-bound yeast, bacterial and mammalian ribosomes.	RESULTS
0	3	40S	complex_assembly	40S head swivel	RESULTS
4	8	head	structure_element	40S head swivel	RESULTS
15	18	40S	complex_assembly	The pattern of 40S head swivel between the structures is different from that of intersubunit rotation (Figures 2c and d; see also Figure 2—source data 1).	RESULTS
19	23	head	structure_element	The pattern of 40S head swivel between the structures is different from that of intersubunit rotation (Figures 2c and d; see also Figure 2—source data 1).	RESULTS
43	53	structures	evidence	The pattern of 40S head swivel between the structures is different from that of intersubunit rotation (Figures 2c and d; see also Figure 2—source data 1).	RESULTS
45	49	head	structure_element	As with the intersubunit rotation, the small head swivel (~1°) in the non-rotated Structure V is closest to that in the 80S•2tRNA•mRNA post-translocation ribosome.	RESULTS
70	81	non-rotated	protein_state	As with the intersubunit rotation, the small head swivel (~1°) in the non-rotated Structure V is closest to that in the 80S•2tRNA•mRNA post-translocation ribosome.	RESULTS
82	93	Structure V	evidence	As with the intersubunit rotation, the small head swivel (~1°) in the non-rotated Structure V is closest to that in the 80S•2tRNA•mRNA post-translocation ribosome.	RESULTS
120	134	80S•2tRNA•mRNA	complex_assembly	As with the intersubunit rotation, the small head swivel (~1°) in the non-rotated Structure V is closest to that in the 80S•2tRNA•mRNA post-translocation ribosome.	RESULTS
135	153	post-translocation	protein_state	As with the intersubunit rotation, the small head swivel (~1°) in the non-rotated Structure V is closest to that in the 80S•2tRNA•mRNA post-translocation ribosome.	RESULTS
154	162	ribosome	complex_assembly	As with the intersubunit rotation, the small head swivel (~1°) in the non-rotated Structure V is closest to that in the 80S•2tRNA•mRNA post-translocation ribosome.	RESULTS
15	32	pre-translocation	protein_state	However in the pre-translocation intermediates (from Structure I to IV), the beak of the head domain first turns toward the large subunit and then backs off (Figure 2—figure supplement 1).	RESULTS
53	70	Structure I to IV	evidence	However in the pre-translocation intermediates (from Structure I to IV), the beak of the head domain first turns toward the large subunit and then backs off (Figure 2—figure supplement 1).	RESULTS
89	93	head	structure_element	However in the pre-translocation intermediates (from Structure I to IV), the beak of the head domain first turns toward the large subunit and then backs off (Figure 2—figure supplement 1).	RESULTS
124	137	large subunit	structure_element	However in the pre-translocation intermediates (from Structure I to IV), the beak of the head domain first turns toward the large subunit and then backs off (Figure 2—figure supplement 1).	RESULTS
4	8	head	structure_element	The head samples a mid-swiveled position in Structure I (12°), then a highly-swiveled position in Structures II and III (17°) and a less swiveled position in Structure IV (14°).	RESULTS
19	31	mid-swiveled	protein_state	The head samples a mid-swiveled position in Structure I (12°), then a highly-swiveled position in Structures II and III (17°) and a less swiveled position in Structure IV (14°).	RESULTS
44	55	Structure I	evidence	The head samples a mid-swiveled position in Structure I (12°), then a highly-swiveled position in Structures II and III (17°) and a less swiveled position in Structure IV (14°).	RESULTS
70	85	highly-swiveled	protein_state	The head samples a mid-swiveled position in Structure I (12°), then a highly-swiveled position in Structures II and III (17°) and a less swiveled position in Structure IV (14°).	RESULTS
98	119	Structures II and III	evidence	The head samples a mid-swiveled position in Structure I (12°), then a highly-swiveled position in Structures II and III (17°) and a less swiveled position in Structure IV (14°).	RESULTS
132	145	less swiveled	protein_state	The head samples a mid-swiveled position in Structure I (12°), then a highly-swiveled position in Structures II and III (17°) and a less swiveled position in Structure IV (14°).	RESULTS
158	170	Structure IV	evidence	The head samples a mid-swiveled position in Structure I (12°), then a highly-swiveled position in Structures II and III (17°) and a less swiveled position in Structure IV (14°).	RESULTS
12	16	head	structure_element	The maximum head swivel is observed in the mid-rotated complexes II and III, in which PKI transitions from the A to P site, while eEF2 occupies the A site partially.	RESULTS
43	54	mid-rotated	protein_state	The maximum head swivel is observed in the mid-rotated complexes II and III, in which PKI transitions from the A to P site, while eEF2 occupies the A site partially.	RESULTS
65	75	II and III	evidence	The maximum head swivel is observed in the mid-rotated complexes II and III, in which PKI transitions from the A to P site, while eEF2 occupies the A site partially.	RESULTS
86	89	PKI	structure_element	The maximum head swivel is observed in the mid-rotated complexes II and III, in which PKI transitions from the A to P site, while eEF2 occupies the A site partially.	RESULTS
111	122	A to P site	site	The maximum head swivel is observed in the mid-rotated complexes II and III, in which PKI transitions from the A to P site, while eEF2 occupies the A site partially.	RESULTS
130	134	eEF2	protein	The maximum head swivel is observed in the mid-rotated complexes II and III, in which PKI transitions from the A to P site, while eEF2 occupies the A site partially.	RESULTS
148	154	A site	site	The maximum head swivel is observed in the mid-rotated complexes II and III, in which PKI transitions from the A to P site, while eEF2 occupies the A site partially.	RESULTS
29	40	mid-rotated	protein_state	By comparison, the similarly mid-rotated (4°) 80S•TSV IRES initiation complex, in the absence of eEF2, adopts a mid-swiveled position (~10°) (Figure 2c).	RESULTS
46	58	80S•TSV IRES	complex_assembly	By comparison, the similarly mid-rotated (4°) 80S•TSV IRES initiation complex, in the absence of eEF2, adopts a mid-swiveled position (~10°) (Figure 2c).	RESULTS
59	69	initiation	protein_state	By comparison, the similarly mid-rotated (4°) 80S•TSV IRES initiation complex, in the absence of eEF2, adopts a mid-swiveled position (~10°) (Figure 2c).	RESULTS
86	96	absence of	protein_state	By comparison, the similarly mid-rotated (4°) 80S•TSV IRES initiation complex, in the absence of eEF2, adopts a mid-swiveled position (~10°) (Figure 2c).	RESULTS
97	101	eEF2	protein	By comparison, the similarly mid-rotated (4°) 80S•TSV IRES initiation complex, in the absence of eEF2, adopts a mid-swiveled position (~10°) (Figure 2c).	RESULTS
112	124	mid-swiveled	protein_state	By comparison, the similarly mid-rotated (4°) 80S•TSV IRES initiation complex, in the absence of eEF2, adopts a mid-swiveled position (~10°) (Figure 2c).	RESULTS
32	36	eEF2	protein	These observations suggest that eEF2 is necessary for inducing or stabilizing the large head swivel of the 40S subunit characteristic for IRES translocation intermediates.	RESULTS
88	92	head	structure_element	These observations suggest that eEF2 is necessary for inducing or stabilizing the large head swivel of the 40S subunit characteristic for IRES translocation intermediates.	RESULTS
107	110	40S	complex_assembly	These observations suggest that eEF2 is necessary for inducing or stabilizing the large head swivel of the 40S subunit characteristic for IRES translocation intermediates.	RESULTS
111	118	subunit	structure_element	These observations suggest that eEF2 is necessary for inducing or stabilizing the large head swivel of the 40S subunit characteristic for IRES translocation intermediates.	RESULTS
138	142	IRES	site	These observations suggest that eEF2 is necessary for inducing or stabilizing the large head swivel of the 40S subunit characteristic for IRES translocation intermediates.	RESULTS
0	4	IRES	site	IRES rearrangements	RESULTS
18	21	TSV	species	Comparison of the TSV IRES and eEF2 positions in Structures I through V.	FIG
22	26	IRES	site	Comparison of the TSV IRES and eEF2 positions in Structures I through V.	FIG
31	35	eEF2	protein	Comparison of the TSV IRES and eEF2 positions in Structures I through V.	FIG
49	71	Structures I through V	evidence	Comparison of the TSV IRES and eEF2 positions in Structures I through V.	FIG
21	25	IRES	site	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
30	34	eEF2	protein	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
42	52	initiation	protein_state	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
54	71	pre-translocation	protein_state	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
73	74	I	evidence	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
80	98	post-translocation	protein_state	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
100	101	V	evidence	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
127	131	body	structure_element	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
139	142	40S	complex_assembly	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
143	150	subunit	structure_element	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
143	150	subunit	structure_element	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
184	188	IRES	site	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
193	197	eEF2	protein	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
205	215	initiation	protein_state	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
223	227	INIT	complex_assembly	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
270	284	II, III and IV	evidence	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
303	307	body	structure_element	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
315	318	40S	complex_assembly	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
319	326	subunit	structure_element	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
319	326	subunit	structure_element	(a) Positions of the IRES and eEF2 in the initiation, pre-translocation (I) and post-translocation (V) states, relative to the body of the 40S subunit (not shown) (b) Positions of the IRES and eEF2 in the initiation state (INIT) and intermediate steps of translocation (II, III and IV), relative to the body of the 40S subunit (not shown).	FIG
33	54	structural alignments	experimental_method	 Superpositions were obtained by structural alignments of the 18S rRNAs excluding the head domains (nt 1150–1620).	FIG
62	71	18S rRNAs	chemical	 Superpositions were obtained by structural alignments of the 18S rRNAs excluding the head domains (nt 1150–1620).	FIG
86	90	head	structure_element	 Superpositions were obtained by structural alignments of the 18S rRNAs excluding the head domains (nt 1150–1620).	FIG
103	112	1150–1620	residue_range	 Superpositions were obtained by structural alignments of the 18S rRNAs excluding the head domains (nt 1150–1620).	FIG
17	21	IRES	site	Positions of the IRES relative to proteins uS7, uS11 and eS25.	FIG
43	46	uS7	protein	Positions of the IRES relative to proteins uS7, uS11 and eS25.	FIG
48	52	uS11	protein	Positions of the IRES relative to proteins uS7, uS11 and eS25.	FIG
57	61	eS25	protein	Positions of the IRES relative to proteins uS7, uS11 and eS25.	FIG
10	14	IRES	site	(a) Intra-IRES rearrangements from the 80S*IRES initiation structure (INIT; PDB 3J6Y,) to Structures I through V. For each structure (shown in red), the conformation from a preceding structure is shown in light red for comparison.	FIG
39	47	80S*IRES	complex_assembly	(a) Intra-IRES rearrangements from the 80S*IRES initiation structure (INIT; PDB 3J6Y,) to Structures I through V. For each structure (shown in red), the conformation from a preceding structure is shown in light red for comparison.	FIG
48	58	initiation	protein_state	(a) Intra-IRES rearrangements from the 80S*IRES initiation structure (INIT; PDB 3J6Y,) to Structures I through V. For each structure (shown in red), the conformation from a preceding structure is shown in light red for comparison.	FIG
59	68	structure	evidence	(a) Intra-IRES rearrangements from the 80S*IRES initiation structure (INIT; PDB 3J6Y,) to Structures I through V. For each structure (shown in red), the conformation from a preceding structure is shown in light red for comparison.	FIG
70	74	INIT	complex_assembly	(a) Intra-IRES rearrangements from the 80S*IRES initiation structure (INIT; PDB 3J6Y,) to Structures I through V. For each structure (shown in red), the conformation from a preceding structure is shown in light red for comparison.	FIG
90	112	Structures I through V	evidence	(a) Intra-IRES rearrangements from the 80S*IRES initiation structure (INIT; PDB 3J6Y,) to Structures I through V. For each structure (shown in red), the conformation from a preceding structure is shown in light red for comparison.	FIG
123	132	structure	evidence	(a) Intra-IRES rearrangements from the 80S*IRES initiation structure (INIT; PDB 3J6Y,) to Structures I through V. For each structure (shown in red), the conformation from a preceding structure is shown in light red for comparison.	FIG
183	192	structure	evidence	(a) Intra-IRES rearrangements from the 80S*IRES initiation structure (INIT; PDB 3J6Y,) to Structures I through V. For each structure (shown in red), the conformation from a preceding structure is shown in light red for comparison.	FIG
0	14	Superpositions	experimental_method	Superpositions were obtained by structural alignments of 18S rRNA.	FIG
32	53	structural alignments	experimental_method	Superpositions were obtained by structural alignments of 18S rRNA.	FIG
57	65	18S rRNA	chemical	Superpositions were obtained by structural alignments of 18S rRNA.	FIG
21	25	IRES	site	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
30	34	eEF2	protein	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
66	79	P- and E-site	site	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
80	85	tRNAs	chemical	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
93	101	80S•tRNA	complex_assembly	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
132	136	IRES	site	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
158	162	uS11	protein	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
164	176	40S platform	site	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
182	185	uS7	protein	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
190	194	eS25	protein	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
196	199	40S	complex_assembly	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
200	204	head	structure_element	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
231	240	5′ domain	structure_element	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
248	252	IRES	site	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
260	270	initiation	protein_state	(b) Positions of the IRES and eEF2 relative to those of classical P- and E-site tRNAs in the 80S•tRNA complex. (c) Positions of the IRES relative to proteins uS11 (40S platform) and uS7 and eS25 (40S head), which interact with the 5′ domain of the IRES in the initiation state (left panel).	FIG
15	29	superpositions	experimental_method	In all panels, superpositions were obtained by structural alignments of the 18S rRNAs.	FIG
47	68	structural alignments	experimental_method	In all panels, superpositions were obtained by structural alignments of the 18S rRNAs.	FIG
76	85	18S rRNAs	chemical	In all panels, superpositions were obtained by structural alignments of the 18S rRNAs.	FIG
26	36	initiation	protein_state	Ribosomal proteins of the initiation state are shown in gray for comparison.	FIG
17	24	L1stalk	structure_element	Positions of the L1stalk, tRNA and TSV IRES relative to proteins uS7 and eS25, in 80S•tRNA structures and 80S•IRES structures I and V (this work).	FIG
26	30	tRNA	chemical	Positions of the L1stalk, tRNA and TSV IRES relative to proteins uS7 and eS25, in 80S•tRNA structures and 80S•IRES structures I and V (this work).	FIG
35	38	TSV	species	Positions of the L1stalk, tRNA and TSV IRES relative to proteins uS7 and eS25, in 80S•tRNA structures and 80S•IRES structures I and V (this work).	FIG
39	43	IRES	site	Positions of the L1stalk, tRNA and TSV IRES relative to proteins uS7 and eS25, in 80S•tRNA structures and 80S•IRES structures I and V (this work).	FIG
65	68	uS7	protein	Positions of the L1stalk, tRNA and TSV IRES relative to proteins uS7 and eS25, in 80S•tRNA structures and 80S•IRES structures I and V (this work).	FIG
73	77	eS25	protein	Positions of the L1stalk, tRNA and TSV IRES relative to proteins uS7 and eS25, in 80S•tRNA structures and 80S•IRES structures I and V (this work).	FIG
82	90	80S•tRNA	complex_assembly	Positions of the L1stalk, tRNA and TSV IRES relative to proteins uS7 and eS25, in 80S•tRNA structures and 80S•IRES structures I and V (this work).	FIG
91	101	structures	evidence	Positions of the L1stalk, tRNA and TSV IRES relative to proteins uS7 and eS25, in 80S•tRNA structures and 80S•IRES structures I and V (this work).	FIG
106	114	80S•IRES	complex_assembly	Positions of the L1stalk, tRNA and TSV IRES relative to proteins uS7 and eS25, in 80S•tRNA structures and 80S•IRES structures I and V (this work).	FIG
115	133	structures I and V	evidence	Positions of the L1stalk, tRNA and TSV IRES relative to proteins uS7 and eS25, in 80S•tRNA structures and 80S•IRES structures I and V (this work).	FIG
45	51	E site	site	The view shows the vicinity of the ribosomal E site.	FIG
0	8	Loop 1.1	structure_element	Loop 1.1 and stem loops 4 and 5 of the IRES are labeled.	FIG
13	31	stem loops 4 and 5	structure_element	Loop 1.1 and stem loops 4 and 5 of the IRES are labeled.	FIG
39	43	IRES	site	Loop 1.1 and stem loops 4 and 5 of the IRES are labeled.	FIG
20	38	stem loops 4 and 5	structure_element	Interactions of the stem loops 4 and 5 of the TSV with proteins uS7 and eS25.	FIG
46	49	TSV	species	Interactions of the stem loops 4 and 5 of the TSV with proteins uS7 and eS25.	FIG
64	67	uS7	protein	Interactions of the stem loops 4 and 5 of the TSV with proteins uS7 and eS25.	FIG
72	76	eS25	protein	Interactions of the stem loops 4 and 5 of the TSV with proteins uS7 and eS25.	FIG
29	35	loop 3	structure_element	Position and interactions of loop 3 (variable loop region) of the PKI domain in Structure V (this work) resembles those of the anticodon stem loop of the E-site tRNA (blue) in the 80S•2tRNA•mRNA complex.	FIG
37	57	variable loop region	structure_element	Position and interactions of loop 3 (variable loop region) of the PKI domain in Structure V (this work) resembles those of the anticodon stem loop of the E-site tRNA (blue) in the 80S•2tRNA•mRNA complex.	FIG
66	69	PKI	structure_element	Position and interactions of loop 3 (variable loop region) of the PKI domain in Structure V (this work) resembles those of the anticodon stem loop of the E-site tRNA (blue) in the 80S•2tRNA•mRNA complex.	FIG
80	91	Structure V	evidence	Position and interactions of loop 3 (variable loop region) of the PKI domain in Structure V (this work) resembles those of the anticodon stem loop of the E-site tRNA (blue) in the 80S•2tRNA•mRNA complex.	FIG
127	146	anticodon stem loop	structure_element	Position and interactions of loop 3 (variable loop region) of the PKI domain in Structure V (this work) resembles those of the anticodon stem loop of the E-site tRNA (blue) in the 80S•2tRNA•mRNA complex.	FIG
154	160	E-site	site	Position and interactions of loop 3 (variable loop region) of the PKI domain in Structure V (this work) resembles those of the anticodon stem loop of the E-site tRNA (blue) in the 80S•2tRNA•mRNA complex.	FIG
161	165	tRNA	chemical	Position and interactions of loop 3 (variable loop region) of the PKI domain in Structure V (this work) resembles those of the anticodon stem loop of the E-site tRNA (blue) in the 80S•2tRNA•mRNA complex.	FIG
180	194	80S•2tRNA•mRNA	complex_assembly	Position and interactions of loop 3 (variable loop region) of the PKI domain in Structure V (this work) resembles those of the anticodon stem loop of the E-site tRNA (blue) in the 80S•2tRNA•mRNA complex.	FIG
13	18	tRNAs	chemical	Positions of tRNAs and the TSV IRES relative to the A-site finger (blue, nt 1008–1043 of 25S rRNA) and the P site of the large subunit, comprising helix 84 of 25S rRNA (nt.	FIG
27	30	TSV	species	Positions of tRNAs and the TSV IRES relative to the A-site finger (blue, nt 1008–1043 of 25S rRNA) and the P site of the large subunit, comprising helix 84 of 25S rRNA (nt.	FIG
31	35	IRES	site	Positions of tRNAs and the TSV IRES relative to the A-site finger (blue, nt 1008–1043 of 25S rRNA) and the P site of the large subunit, comprising helix 84 of 25S rRNA (nt.	FIG
52	65	A-site finger	structure_element	Positions of tRNAs and the TSV IRES relative to the A-site finger (blue, nt 1008–1043 of 25S rRNA) and the P site of the large subunit, comprising helix 84 of 25S rRNA (nt.	FIG
76	85	1008–1043	residue_range	Positions of tRNAs and the TSV IRES relative to the A-site finger (blue, nt 1008–1043 of 25S rRNA) and the P site of the large subunit, comprising helix 84 of 25S rRNA (nt.	FIG
89	97	25S rRNA	chemical	Positions of tRNAs and the TSV IRES relative to the A-site finger (blue, nt 1008–1043 of 25S rRNA) and the P site of the large subunit, comprising helix 84 of 25S rRNA (nt.	FIG
107	113	P site	site	Positions of tRNAs and the TSV IRES relative to the A-site finger (blue, nt 1008–1043 of 25S rRNA) and the P site of the large subunit, comprising helix 84 of 25S rRNA (nt.	FIG
121	134	large subunit	structure_element	Positions of tRNAs and the TSV IRES relative to the A-site finger (blue, nt 1008–1043 of 25S rRNA) and the P site of the large subunit, comprising helix 84 of 25S rRNA (nt.	FIG
147	155	helix 84	structure_element	Positions of tRNAs and the TSV IRES relative to the A-site finger (blue, nt 1008–1043 of 25S rRNA) and the P site of the large subunit, comprising helix 84 of 25S rRNA (nt.	FIG
159	167	25S rRNA	chemical	Positions of tRNAs and the TSV IRES relative to the A-site finger (blue, nt 1008–1043 of 25S rRNA) and the P site of the large subunit, comprising helix 84 of 25S rRNA (nt.	FIG
0	9	2668–2687	residue_range	2668–2687) and protein uL5 (collectively labeled as central protuberance, CP, in the upper-row first figure, and individually labeled in the lower-row first figure).	FIG
23	26	uL5	protein	2668–2687) and protein uL5 (collectively labeled as central protuberance, CP, in the upper-row first figure, and individually labeled in the lower-row first figure).	FIG
52	72	central protuberance	structure_element	2668–2687) and protein uL5 (collectively labeled as central protuberance, CP, in the upper-row first figure, and individually labeled in the lower-row first figure).	FIG
74	76	CP	structure_element	2668–2687) and protein uL5 (collectively labeled as central protuberance, CP, in the upper-row first figure, and individually labeled in the lower-row first figure).	FIG
0	10	Structures	evidence	Structures of translocation complexes of the bacterial 70S ribosome bound with two tRNAs and yeast 80S complexes with tRNAs are shown in the upper row and labeled.	FIG
45	54	bacterial	taxonomy_domain	Structures of translocation complexes of the bacterial 70S ribosome bound with two tRNAs and yeast 80S complexes with tRNAs are shown in the upper row and labeled.	FIG
55	67	70S ribosome	complex_assembly	Structures of translocation complexes of the bacterial 70S ribosome bound with two tRNAs and yeast 80S complexes with tRNAs are shown in the upper row and labeled.	FIG
68	78	bound with	protein_state	Structures of translocation complexes of the bacterial 70S ribosome bound with two tRNAs and yeast 80S complexes with tRNAs are shown in the upper row and labeled.	FIG
83	88	tRNAs	chemical	Structures of translocation complexes of the bacterial 70S ribosome bound with two tRNAs and yeast 80S complexes with tRNAs are shown in the upper row and labeled.	FIG
93	98	yeast	taxonomy_domain	Structures of translocation complexes of the bacterial 70S ribosome bound with two tRNAs and yeast 80S complexes with tRNAs are shown in the upper row and labeled.	FIG
99	102	80S	complex_assembly	Structures of translocation complexes of the bacterial 70S ribosome bound with two tRNAs and yeast 80S complexes with tRNAs are shown in the upper row and labeled.	FIG
103	117	complexes with	protein_state	Structures of translocation complexes of the bacterial 70S ribosome bound with two tRNAs and yeast 80S complexes with tRNAs are shown in the upper row and labeled.	FIG
118	123	tRNAs	chemical	Structures of translocation complexes of the bacterial 70S ribosome bound with two tRNAs and yeast 80S complexes with tRNAs are shown in the upper row and labeled.	FIG
0	10	Structures	evidence	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the lower row and labeled.	FIG
14	22	80S•IRES	complex_assembly	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the lower row and labeled.	FIG
40	50	absence of	protein_state	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the lower row and labeled.	FIG
51	55	eEF2	protein	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the lower row and labeled.	FIG
57	61	INIT	complex_assembly	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the lower row and labeled.	FIG
85	96	presence of	protein_state	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the lower row and labeled.	FIG
97	101	eEF2	protein	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the lower row and labeled.	FIG
20	23	TSV	species	Interactions of the TSV IRES with uL5 and eL42.	FIG
24	28	IRES	site	Interactions of the TSV IRES with uL5 and eL42.	FIG
34	37	uL5	protein	Interactions of the TSV IRES with uL5 and eL42.	FIG
42	46	eL42	protein	Interactions of the TSV IRES with uL5 and eL42.	FIG
0	10	Structures	evidence	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the upper row and labeled.	FIG
14	22	80S•IRES	complex_assembly	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the upper row and labeled.	FIG
40	50	absence of	protein_state	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the upper row and labeled.	FIG
51	55	eEF2	protein	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the upper row and labeled.	FIG
57	61	INIT	complex_assembly	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the upper row and labeled.	FIG
85	96	presence of	protein_state	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the upper row and labeled.	FIG
97	101	eEF2	protein	Structures of 80S•IRES complexes in the absence of eEF2 (INIT; PDB 3J6Y,) and in the presence of eEF2 (this work) are shown in the upper row and labeled.	FIG
0	10	Structures	evidence	Structures of the 80S complexes with tRNAs are shown in the lower row in a view similar to that for the 80S•IRES complex.	FIG
18	21	80S	complex_assembly	Structures of the 80S complexes with tRNAs are shown in the lower row in a view similar to that for the 80S•IRES complex.	FIG
22	36	complexes with	protein_state	Structures of the 80S complexes with tRNAs are shown in the lower row in a view similar to that for the 80S•IRES complex.	FIG
37	42	tRNAs	chemical	Structures of the 80S complexes with tRNAs are shown in the lower row in a view similar to that for the 80S•IRES complex.	FIG
104	112	80S•IRES	complex_assembly	Structures of the 80S complexes with tRNAs are shown in the lower row in a view similar to that for the 80S•IRES complex.	FIG
17	21	IRES	site	Positions of the IRES relative to eEF2 and elements of the ribosome in Structures I through V.	FIG
34	38	eEF2	protein	Positions of the IRES relative to eEF2 and elements of the ribosome in Structures I through V.	FIG
59	67	ribosome	complex_assembly	Positions of the IRES relative to eEF2 and elements of the ribosome in Structures I through V.	FIG
71	93	Structures I through V	evidence	Positions of the IRES relative to eEF2 and elements of the ribosome in Structures I through V.	FIG
14	23	structure	evidence	(a) Secondary structure of the TSV IRES.	FIG
31	34	TSV	species	(a) Secondary structure of the TSV IRES.	FIG
35	39	IRES	site	(a) Secondary structure of the TSV IRES.	FIG
5	8	TSV	species	 The TSV IRES comprises two domains: the 5' domain (blue) and the PKI domain (red).	FIG
9	13	IRES	site	 The TSV IRES comprises two domains: the 5' domain (blue) and the PKI domain (red).	FIG
41	50	5' domain	structure_element	 The TSV IRES comprises two domains: the 5' domain (blue) and the PKI domain (red).	FIG
66	69	PKI	structure_element	 The TSV IRES comprises two domains: the 5' domain (blue) and the PKI domain (red).	FIG
4	22	open reading frame	structure_element	The open reading frame (gray) is immediately following pseudoknot I (PKI).	FIG
55	67	pseudoknot I	structure_element	The open reading frame (gray) is immediately following pseudoknot I (PKI).	FIG
69	72	PKI	structure_element	The open reading frame (gray) is immediately following pseudoknot I (PKI).	FIG
22	31	structure	evidence	(b) Three-dimensional structure of the TSV IRES (Structure II).	FIG
39	42	TSV	species	(b) Three-dimensional structure of the TSV IRES (Structure II).	FIG
43	47	IRES	site	(b) Three-dimensional structure of the TSV IRES (Structure II).	FIG
49	61	Structure II	evidence	(b) Three-dimensional structure of the TSV IRES (Structure II).	FIG
16	26	stem loops	structure_element	Pseudoknots and stem loops are labeled and colored as in (a).	FIG
21	25	IRES	site	(c) Positions of the IRES and eEF2 on the small subunit in Structures I to V. The initiation-state IRES is shown in gray.	FIG
30	34	eEF2	protein	(c) Positions of the IRES and eEF2 on the small subunit in Structures I to V. The initiation-state IRES is shown in gray.	FIG
42	55	small subunit	structure_element	(c) Positions of the IRES and eEF2 on the small subunit in Structures I to V. The initiation-state IRES is shown in gray.	FIG
59	76	Structures I to V	evidence	(c) Positions of the IRES and eEF2 on the small subunit in Structures I to V. The initiation-state IRES is shown in gray.	FIG
82	92	initiation	protein_state	(c) Positions of the IRES and eEF2 on the small subunit in Structures I to V. The initiation-state IRES is shown in gray.	FIG
99	103	IRES	site	(c) Positions of the IRES and eEF2 on the small subunit in Structures I to V. The initiation-state IRES is shown in gray.	FIG
61	65	eEF2	protein	 The insert shows density for interaction of diphthamide 699 (eEF2; green) with the codon-anticodon-like helix (PKI; red) in Structure V. (d and e) Density of the P site in Structure V shows that interactions of PKI with the 18S rRNA nucleotides (c) are nearly identical to those in the P site of the 2tRNA•mRNA-bound 70S ribosome (d).	FIG
111	114	PKI	structure_element	 The insert shows density for interaction of diphthamide 699 (eEF2; green) with the codon-anticodon-like helix (PKI; red) in Structure V. (d and e) Density of the P site in Structure V shows that interactions of PKI with the 18S rRNA nucleotides (c) are nearly identical to those in the P site of the 2tRNA•mRNA-bound 70S ribosome (d).	FIG
8	17	structure	evidence	In each structure, the TSV IRES adopts a distinct conformation in the intersubunit space of the ribosome (Figures 3 and 4).	RESULTS
23	26	TSV	species	In each structure, the TSV IRES adopts a distinct conformation in the intersubunit space of the ribosome (Figures 3 and 4).	RESULTS
27	31	IRES	site	In each structure, the TSV IRES adopts a distinct conformation in the intersubunit space of the ribosome (Figures 3 and 4).	RESULTS
96	104	ribosome	complex_assembly	In each structure, the TSV IRES adopts a distinct conformation in the intersubunit space of the ribosome (Figures 3 and 4).	RESULTS
4	8	IRES	site	The IRES (nt 6758–6952) consists of two globular parts (Figure 3a): the 5’-region (domains I and II, nt 6758–6888) and the PKI domain (domain III, nt 6889–6952).	RESULTS
13	22	6758–6952	residue_range	The IRES (nt 6758–6952) consists of two globular parts (Figure 3a): the 5’-region (domains I and II, nt 6758–6888) and the PKI domain (domain III, nt 6889–6952).	RESULTS
72	81	5’-region	structure_element	The IRES (nt 6758–6952) consists of two globular parts (Figure 3a): the 5’-region (domains I and II, nt 6758–6888) and the PKI domain (domain III, nt 6889–6952).	RESULTS
91	92	I	structure_element	The IRES (nt 6758–6952) consists of two globular parts (Figure 3a): the 5’-region (domains I and II, nt 6758–6888) and the PKI domain (domain III, nt 6889–6952).	RESULTS
97	99	II	structure_element	The IRES (nt 6758–6952) consists of two globular parts (Figure 3a): the 5’-region (domains I and II, nt 6758–6888) and the PKI domain (domain III, nt 6889–6952).	RESULTS
104	113	6758–6888	residue_range	The IRES (nt 6758–6952) consists of two globular parts (Figure 3a): the 5’-region (domains I and II, nt 6758–6888) and the PKI domain (domain III, nt 6889–6952).	RESULTS
123	126	PKI	structure_element	The IRES (nt 6758–6952) consists of two globular parts (Figure 3a): the 5’-region (domains I and II, nt 6758–6888) and the PKI domain (domain III, nt 6889–6952).	RESULTS
142	145	III	structure_element	The IRES (nt 6758–6952) consists of two globular parts (Figure 3a): the 5’-region (domains I and II, nt 6758–6888) and the PKI domain (domain III, nt 6889–6952).	RESULTS
150	159	6889–6952	residue_range	The IRES (nt 6758–6952) consists of two globular parts (Figure 3a): the 5’-region (domains I and II, nt 6758–6888) and the PKI domain (domain III, nt 6889–6952).	RESULTS
29	30	I	structure_element	We collectively term domains I and II the 5’ domain.	RESULTS
35	37	II	structure_element	We collectively term domains I and II the 5’ domain.	RESULTS
42	51	5’ domain	structure_element	We collectively term domains I and II the 5’ domain.	RESULTS
4	7	PKI	structure_element	The PKI domain comprises PKI and stem loop 3 (SL3), which stacks on top of the stem of PKI.	RESULTS
25	28	PKI	structure_element	The PKI domain comprises PKI and stem loop 3 (SL3), which stacks on top of the stem of PKI.	RESULTS
33	44	stem loop 3	structure_element	The PKI domain comprises PKI and stem loop 3 (SL3), which stacks on top of the stem of PKI.	RESULTS
46	49	SL3	structure_element	The PKI domain comprises PKI and stem loop 3 (SL3), which stacks on top of the stem of PKI.	RESULTS
87	90	PKI	structure_element	The PKI domain comprises PKI and stem loop 3 (SL3), which stacks on top of the stem of PKI.	RESULTS
46	49	PKI	structure_element	The 6953GCU triplet immediately following the PKI domain is the first codon of the open reading frame.	RESULTS
83	101	open reading frame	structure_element	The 6953GCU triplet immediately following the PKI domain is the first codon of the open reading frame.	RESULTS
7	16	eEF2-free	protein_state	In the eEF2-free 80S•IRES initiation complex (INIT), the bulk of the 5’-domain (nt.	RESULTS
17	25	80S•IRES	complex_assembly	In the eEF2-free 80S•IRES initiation complex (INIT), the bulk of the 5’-domain (nt.	RESULTS
26	36	initiation	protein_state	In the eEF2-free 80S•IRES initiation complex (INIT), the bulk of the 5’-domain (nt.	RESULTS
46	50	INIT	complex_assembly	In the eEF2-free 80S•IRES initiation complex (INIT), the bulk of the 5’-domain (nt.	RESULTS
69	78	5’-domain	structure_element	In the eEF2-free 80S•IRES initiation complex (INIT), the bulk of the 5’-domain (nt.	RESULTS
0	9	6758–6888	residue_range	6758–6888) binds near the E site, contacting the ribosome mostly by means of three protruding structural elements: the L1.1 region and stem loops 4 and 5 (SL4 and SL5).	RESULTS
26	32	E site	site	6758–6888) binds near the E site, contacting the ribosome mostly by means of three protruding structural elements: the L1.1 region and stem loops 4 and 5 (SL4 and SL5).	RESULTS
49	57	ribosome	complex_assembly	6758–6888) binds near the E site, contacting the ribosome mostly by means of three protruding structural elements: the L1.1 region and stem loops 4 and 5 (SL4 and SL5).	RESULTS
119	130	L1.1 region	structure_element	6758–6888) binds near the E site, contacting the ribosome mostly by means of three protruding structural elements: the L1.1 region and stem loops 4 and 5 (SL4 and SL5).	RESULTS
135	153	stem loops 4 and 5	structure_element	6758–6888) binds near the E site, contacting the ribosome mostly by means of three protruding structural elements: the L1.1 region and stem loops 4 and 5 (SL4 and SL5).	RESULTS
155	158	SL4	structure_element	6758–6888) binds near the E site, contacting the ribosome mostly by means of three protruding structural elements: the L1.1 region and stem loops 4 and 5 (SL4 and SL5).	RESULTS
163	166	SL5	structure_element	6758–6888) binds near the E site, contacting the ribosome mostly by means of three protruding structural elements: the L1.1 region and stem loops 4 and 5 (SL4 and SL5).	RESULTS
3	21	Structures I to IV	evidence	In Structures I to IV, these contacts remain as in the initiation complex (Figure 1a).	RESULTS
55	73	initiation complex	complex_assembly	In Structures I to IV, these contacts remain as in the initiation complex (Figure 1a).	RESULTS
18	29	L1.1 region	structure_element	Specifically, the L1.1 region interacts with the L1 stalk of the large subunit, while SL4 and SL5 bind at the side of the 40S head and interact with proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2 and Figure 3—figure supplement 3; ribosomal proteins are termed according to).	RESULTS
49	57	L1 stalk	structure_element	Specifically, the L1.1 region interacts with the L1 stalk of the large subunit, while SL4 and SL5 bind at the side of the 40S head and interact with proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2 and Figure 3—figure supplement 3; ribosomal proteins are termed according to).	RESULTS
65	78	large subunit	structure_element	Specifically, the L1.1 region interacts with the L1 stalk of the large subunit, while SL4 and SL5 bind at the side of the 40S head and interact with proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2 and Figure 3—figure supplement 3; ribosomal proteins are termed according to).	RESULTS
86	89	SL4	structure_element	Specifically, the L1.1 region interacts with the L1 stalk of the large subunit, while SL4 and SL5 bind at the side of the 40S head and interact with proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2 and Figure 3—figure supplement 3; ribosomal proteins are termed according to).	RESULTS
94	97	SL5	structure_element	Specifically, the L1.1 region interacts with the L1 stalk of the large subunit, while SL4 and SL5 bind at the side of the 40S head and interact with proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2 and Figure 3—figure supplement 3; ribosomal proteins are termed according to).	RESULTS
122	125	40S	complex_assembly	Specifically, the L1.1 region interacts with the L1 stalk of the large subunit, while SL4 and SL5 bind at the side of the 40S head and interact with proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2 and Figure 3—figure supplement 3; ribosomal proteins are termed according to).	RESULTS
126	130	head	structure_element	Specifically, the L1.1 region interacts with the L1 stalk of the large subunit, while SL4 and SL5 bind at the side of the 40S head and interact with proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2 and Figure 3—figure supplement 3; ribosomal proteins are termed according to).	RESULTS
158	161	uS7	protein	Specifically, the L1.1 region interacts with the L1 stalk of the large subunit, while SL4 and SL5 bind at the side of the 40S head and interact with proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2 and Figure 3—figure supplement 3; ribosomal proteins are termed according to).	RESULTS
163	167	uS11	protein	Specifically, the L1.1 region interacts with the L1 stalk of the large subunit, while SL4 and SL5 bind at the side of the 40S head and interact with proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2 and Figure 3—figure supplement 3; ribosomal proteins are termed according to).	RESULTS
172	176	eS25	protein	Specifically, the L1.1 region interacts with the L1 stalk of the large subunit, while SL4 and SL5 bind at the side of the 40S head and interact with proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2 and Figure 3—figure supplement 3; ribosomal proteins are termed according to).	RESULTS
3	18	Structures I-IV	evidence	In Structures I-IV, the minor groove of SL4 (at nt 6840–6846) binds next to an α-helix of uS7, which is rich in positively charged residues (K212, K213, R219 and K222).	RESULTS
24	36	minor groove	site	In Structures I-IV, the minor groove of SL4 (at nt 6840–6846) binds next to an α-helix of uS7, which is rich in positively charged residues (K212, K213, R219 and K222).	RESULTS
40	43	SL4	structure_element	In Structures I-IV, the minor groove of SL4 (at nt 6840–6846) binds next to an α-helix of uS7, which is rich in positively charged residues (K212, K213, R219 and K222).	RESULTS
51	60	6840–6846	residue_range	In Structures I-IV, the minor groove of SL4 (at nt 6840–6846) binds next to an α-helix of uS7, which is rich in positively charged residues (K212, K213, R219 and K222).	RESULTS
79	86	α-helix	structure_element	In Structures I-IV, the minor groove of SL4 (at nt 6840–6846) binds next to an α-helix of uS7, which is rich in positively charged residues (K212, K213, R219 and K222).	RESULTS
90	93	uS7	protein	In Structures I-IV, the minor groove of SL4 (at nt 6840–6846) binds next to an α-helix of uS7, which is rich in positively charged residues (K212, K213, R219 and K222).	RESULTS
141	145	K212	residue_name_number	In Structures I-IV, the minor groove of SL4 (at nt 6840–6846) binds next to an α-helix of uS7, which is rich in positively charged residues (K212, K213, R219 and K222).	RESULTS
147	151	K213	residue_name_number	In Structures I-IV, the minor groove of SL4 (at nt 6840–6846) binds next to an α-helix of uS7, which is rich in positively charged residues (K212, K213, R219 and K222).	RESULTS
153	157	R219	residue_name_number	In Structures I-IV, the minor groove of SL4 (at nt 6840–6846) binds next to an α-helix of uS7, which is rich in positively charged residues (K212, K213, R219 and K222).	RESULTS
162	166	K222	residue_name_number	In Structures I-IV, the minor groove of SL4 (at nt 6840–6846) binds next to an α-helix of uS7, which is rich in positively charged residues (K212, K213, R219 and K222).	RESULTS
11	14	SL4	structure_element	The tip of SL4 binds in the vicinity of R157 in the β-hairpin of uS7 and of Y58 in uS11.	RESULTS
40	44	R157	residue_name_number	The tip of SL4 binds in the vicinity of R157 in the β-hairpin of uS7 and of Y58 in uS11.	RESULTS
52	61	β-hairpin	structure_element	The tip of SL4 binds in the vicinity of R157 in the β-hairpin of uS7 and of Y58 in uS11.	RESULTS
65	68	uS7	protein	The tip of SL4 binds in the vicinity of R157 in the β-hairpin of uS7 and of Y58 in uS11.	RESULTS
76	79	Y58	residue_name_number	The tip of SL4 binds in the vicinity of R157 in the β-hairpin of uS7 and of Y58 in uS11.	RESULTS
83	87	uS11	protein	The tip of SL4 binds in the vicinity of R157 in the β-hairpin of uS7 and of Y58 in uS11.	RESULTS
4	16	minor groove	site	The minor groove of SL5 (at nt 6862–6868) contacts the positively charged region of eS25 (R49, R58 and R68) (Figure 3—figure supplement 4).	RESULTS
20	23	SL5	structure_element	The minor groove of SL5 (at nt 6862–6868) contacts the positively charged region of eS25 (R49, R58 and R68) (Figure 3—figure supplement 4).	RESULTS
31	40	6862–6868	residue_range	The minor groove of SL5 (at nt 6862–6868) contacts the positively charged region of eS25 (R49, R58 and R68) (Figure 3—figure supplement 4).	RESULTS
84	88	eS25	protein	The minor groove of SL5 (at nt 6862–6868) contacts the positively charged region of eS25 (R49, R58 and R68) (Figure 3—figure supplement 4).	RESULTS
90	93	R49	residue_name_number	The minor groove of SL5 (at nt 6862–6868) contacts the positively charged region of eS25 (R49, R58 and R68) (Figure 3—figure supplement 4).	RESULTS
95	98	R58	residue_name_number	The minor groove of SL5 (at nt 6862–6868) contacts the positively charged region of eS25 (R49, R58 and R68) (Figure 3—figure supplement 4).	RESULTS
103	106	R68	residue_name_number	The minor groove of SL5 (at nt 6862–6868) contacts the positively charged region of eS25 (R49, R58 and R68) (Figure 3—figure supplement 4).	RESULTS
3	14	Structure V	evidence	In Structure V, however, the density for SL5 is missing suggesting that SL5 is mobile, while weak SL4 density suggests that SL4 is shifted along the surface of uS7, ~20 Å away from its initial position (Figure 3—figure supplement 2c).	RESULTS
29	36	density	evidence	In Structure V, however, the density for SL5 is missing suggesting that SL5 is mobile, while weak SL4 density suggests that SL4 is shifted along the surface of uS7, ~20 Å away from its initial position (Figure 3—figure supplement 2c).	RESULTS
41	44	SL5	structure_element	In Structure V, however, the density for SL5 is missing suggesting that SL5 is mobile, while weak SL4 density suggests that SL4 is shifted along the surface of uS7, ~20 Å away from its initial position (Figure 3—figure supplement 2c).	RESULTS
72	75	SL5	structure_element	In Structure V, however, the density for SL5 is missing suggesting that SL5 is mobile, while weak SL4 density suggests that SL4 is shifted along the surface of uS7, ~20 Å away from its initial position (Figure 3—figure supplement 2c).	RESULTS
79	85	mobile	protein_state	In Structure V, however, the density for SL5 is missing suggesting that SL5 is mobile, while weak SL4 density suggests that SL4 is shifted along the surface of uS7, ~20 Å away from its initial position (Figure 3—figure supplement 2c).	RESULTS
98	101	SL4	structure_element	In Structure V, however, the density for SL5 is missing suggesting that SL5 is mobile, while weak SL4 density suggests that SL4 is shifted along the surface of uS7, ~20 Å away from its initial position (Figure 3—figure supplement 2c).	RESULTS
102	109	density	evidence	In Structure V, however, the density for SL5 is missing suggesting that SL5 is mobile, while weak SL4 density suggests that SL4 is shifted along the surface of uS7, ~20 Å away from its initial position (Figure 3—figure supplement 2c).	RESULTS
124	127	SL4	structure_element	In Structure V, however, the density for SL5 is missing suggesting that SL5 is mobile, while weak SL4 density suggests that SL4 is shifted along the surface of uS7, ~20 Å away from its initial position (Figure 3—figure supplement 2c).	RESULTS
160	163	uS7	protein	In Structure V, however, the density for SL5 is missing suggesting that SL5 is mobile, while weak SL4 density suggests that SL4 is shifted along the surface of uS7, ~20 Å away from its initial position (Figure 3—figure supplement 2c).	RESULTS
4	15	L1.1 region	structure_element	The L1.1 region remains in contact with the L1 stalk (Figure 3—figure supplement 3).	RESULTS
44	52	L1 stalk	structure_element	The L1.1 region remains in contact with the L1 stalk (Figure 3—figure supplement 3).	RESULTS
0	8	Inchworm	protein_state	Inchworm-like translocation of the TSV IRES.	FIG
35	38	TSV	species	Inchworm-like translocation of the TSV IRES.	FIG
39	43	IRES	site	Inchworm-like translocation of the TSV IRES.	FIG
35	39	IRES	site	Conformations and positions of the IRES in the initiation state and in Structures I-V are shown relative to those of the A-, P- and E-site tRNAs.	FIG
47	57	initiation	protein_state	Conformations and positions of the IRES in the initiation state and in Structures I-V are shown relative to those of the A-, P- and E-site tRNAs.	FIG
71	85	Structures I-V	evidence	Conformations and positions of the IRES in the initiation state and in Structures I-V are shown relative to those of the A-, P- and E-site tRNAs.	FIG
121	138	A-, P- and E-site	site	Conformations and positions of the IRES in the initiation state and in Structures I-V are shown relative to those of the A-, P- and E-site tRNAs.	FIG
139	144	tRNAs	chemical	Conformations and positions of the IRES in the initiation state and in Structures I-V are shown relative to those of the A-, P- and E-site tRNAs.	FIG
25	45	structural alignment	experimental_method	The view was obtained by structural alignment of the body domains of 18S rRNAs of the corresponding 80S structures.	FIG
53	57	body	structure_element	The view was obtained by structural alignment of the body domains of 18S rRNAs of the corresponding 80S structures.	FIG
69	78	18S rRNAs	chemical	The view was obtained by structural alignment of the body domains of 18S rRNAs of the corresponding 80S structures.	FIG
100	103	80S	complex_assembly	The view was obtained by structural alignment of the body domains of 18S rRNAs of the corresponding 80S structures.	FIG
104	114	structures	evidence	The view was obtained by structural alignment of the body domains of 18S rRNAs of the corresponding 80S structures.	FIG
30	34	6848	residue_number	Distances between nucleotides 6848 and 6913 in SL4 and PKI, respectively, are shown (see also Figure 2—source data 1).	FIG
39	43	6913	residue_number	Distances between nucleotides 6848 and 6913 in SL4 and PKI, respectively, are shown (see also Figure 2—source data 1).	FIG
47	50	SL4	structure_element	Distances between nucleotides 6848 and 6913 in SL4 and PKI, respectively, are shown (see also Figure 2—source data 1).	FIG
55	58	PKI	structure_element	Distances between nucleotides 6848 and 6913 in SL4 and PKI, respectively, are shown (see also Figure 2—source data 1).	FIG
17	21	IRES	site	The shape of the IRES changes considerably from the initiation state to Structures I through V, from an extended to compact to extended conformation (Figure 4; see also Figure 3—figure supplement 2a).	RESULTS
52	62	initiation	protein_state	The shape of the IRES changes considerably from the initiation state to Structures I through V, from an extended to compact to extended conformation (Figure 4; see also Figure 3—figure supplement 2a).	RESULTS
72	94	Structures I through V	evidence	The shape of the IRES changes considerably from the initiation state to Structures I through V, from an extended to compact to extended conformation (Figure 4; see also Figure 3—figure supplement 2a).	RESULTS
104	112	extended	protein_state	The shape of the IRES changes considerably from the initiation state to Structures I through V, from an extended to compact to extended conformation (Figure 4; see also Figure 3—figure supplement 2a).	RESULTS
116	123	compact	protein_state	The shape of the IRES changes considerably from the initiation state to Structures I through V, from an extended to compact to extended conformation (Figure 4; see also Figure 3—figure supplement 2a).	RESULTS
127	135	extended	protein_state	The shape of the IRES changes considerably from the initiation state to Structures I through V, from an extended to compact to extended conformation (Figure 4; see also Figure 3—figure supplement 2a).	RESULTS
11	29	Structures I to IV	evidence	Because in Structures I to IV the PKI domain shifts toward the P site, while the 5’ remains unchanged near the E site, the distance between the domains shortens (Figure 4).	RESULTS
34	37	PKI	structure_element	Because in Structures I to IV the PKI domain shifts toward the P site, while the 5’ remains unchanged near the E site, the distance between the domains shortens (Figure 4).	RESULTS
63	69	P site	site	Because in Structures I to IV the PKI domain shifts toward the P site, while the 5’ remains unchanged near the E site, the distance between the domains shortens (Figure 4).	RESULTS
111	117	E site	site	Because in Structures I to IV the PKI domain shifts toward the P site, while the 5’ remains unchanged near the E site, the distance between the domains shortens (Figure 4).	RESULTS
7	15	80S•IRES	complex_assembly	In the 80S•IRES initiation state, the A-site-bound PKI is separated from SL4 by almost 50 Å (Figure 4).	RESULTS
16	26	initiation	protein_state	In the 80S•IRES initiation state, the A-site-bound PKI is separated from SL4 by almost 50 Å (Figure 4).	RESULTS
38	50	A-site-bound	protein_state	In the 80S•IRES initiation state, the A-site-bound PKI is separated from SL4 by almost 50 Å (Figure 4).	RESULTS
51	54	PKI	structure_element	In the 80S•IRES initiation state, the A-site-bound PKI is separated from SL4 by almost 50 Å (Figure 4).	RESULTS
73	76	SL4	structure_element	In the 80S•IRES initiation state, the A-site-bound PKI is separated from SL4 by almost 50 Å (Figure 4).	RESULTS
3	22	Structures I and II	evidence	In Structures I and II, the PKI is partially retracted from the A site and the distance from SL4 shortens to ~35 Å. As PKI moves toward the P site in Structures III and IV, the PKI domain approaches to within ~25 Å of SL4.	RESULTS
28	31	PKI	structure_element	In Structures I and II, the PKI is partially retracted from the A site and the distance from SL4 shortens to ~35 Å. As PKI moves toward the P site in Structures III and IV, the PKI domain approaches to within ~25 Å of SL4.	RESULTS
64	70	A site	site	In Structures I and II, the PKI is partially retracted from the A site and the distance from SL4 shortens to ~35 Å. As PKI moves toward the P site in Structures III and IV, the PKI domain approaches to within ~25 Å of SL4.	RESULTS
93	96	SL4	structure_element	In Structures I and II, the PKI is partially retracted from the A site and the distance from SL4 shortens to ~35 Å. As PKI moves toward the P site in Structures III and IV, the PKI domain approaches to within ~25 Å of SL4.	RESULTS
119	122	PKI	structure_element	In Structures I and II, the PKI is partially retracted from the A site and the distance from SL4 shortens to ~35 Å. As PKI moves toward the P site in Structures III and IV, the PKI domain approaches to within ~25 Å of SL4.	RESULTS
140	146	P site	site	In Structures I and II, the PKI is partially retracted from the A site and the distance from SL4 shortens to ~35 Å. As PKI moves toward the P site in Structures III and IV, the PKI domain approaches to within ~25 Å of SL4.	RESULTS
150	171	Structures III and IV	evidence	In Structures I and II, the PKI is partially retracted from the A site and the distance from SL4 shortens to ~35 Å. As PKI moves toward the P site in Structures III and IV, the PKI domain approaches to within ~25 Å of SL4.	RESULTS
177	180	PKI	structure_element	In Structures I and II, the PKI is partially retracted from the A site and the distance from SL4 shortens to ~35 Å. As PKI moves toward the P site in Structures III and IV, the PKI domain approaches to within ~25 Å of SL4.	RESULTS
218	221	SL4	structure_element	In Structures I and II, the PKI is partially retracted from the A site and the distance from SL4 shortens to ~35 Å. As PKI moves toward the P site in Structures III and IV, the PKI domain approaches to within ~25 Å of SL4.	RESULTS
12	21	5’-domain	structure_element	Because the 5’-domain in the following structure (V) moves by ~20 Å along the 40S head, the IRES returns to an extended conformation (~45 Å) that is similar to that in the 80S•IRES initiation complex.	RESULTS
39	52	structure (V)	evidence	Because the 5’-domain in the following structure (V) moves by ~20 Å along the 40S head, the IRES returns to an extended conformation (~45 Å) that is similar to that in the 80S•IRES initiation complex.	RESULTS
78	81	40S	complex_assembly	Because the 5’-domain in the following structure (V) moves by ~20 Å along the 40S head, the IRES returns to an extended conformation (~45 Å) that is similar to that in the 80S•IRES initiation complex.	RESULTS
82	86	head	structure_element	Because the 5’-domain in the following structure (V) moves by ~20 Å along the 40S head, the IRES returns to an extended conformation (~45 Å) that is similar to that in the 80S•IRES initiation complex.	RESULTS
92	96	IRES	site	Because the 5’-domain in the following structure (V) moves by ~20 Å along the 40S head, the IRES returns to an extended conformation (~45 Å) that is similar to that in the 80S•IRES initiation complex.	RESULTS
111	119	extended	protein_state	Because the 5’-domain in the following structure (V) moves by ~20 Å along the 40S head, the IRES returns to an extended conformation (~45 Å) that is similar to that in the 80S•IRES initiation complex.	RESULTS
172	180	80S•IRES	complex_assembly	Because the 5’-domain in the following structure (V) moves by ~20 Å along the 40S head, the IRES returns to an extended conformation (~45 Å) that is similar to that in the 80S•IRES initiation complex.	RESULTS
181	191	initiation	protein_state	Because the 5’-domain in the following structure (V) moves by ~20 Å along the 40S head, the IRES returns to an extended conformation (~45 Å) that is similar to that in the 80S•IRES initiation complex.	RESULTS
22	26	IRES	site	Rearrangements of the IRES involve restructuring of several interactions with the ribosome.	RESULTS
82	90	ribosome	complex_assembly	Rearrangements of the IRES involve restructuring of several interactions with the ribosome.	RESULTS
3	14	Structure I	evidence	In Structure I, SL3 of the PKI domain is positioned between the A-site finger (nt 1008–1043 of 25S rRNA) and the P site of the 60S subunit, comprising helix 84 of 25S rRNA (nt.	RESULTS
16	19	SL3	structure_element	In Structure I, SL3 of the PKI domain is positioned between the A-site finger (nt 1008–1043 of 25S rRNA) and the P site of the 60S subunit, comprising helix 84 of 25S rRNA (nt.	RESULTS
27	30	PKI	structure_element	In Structure I, SL3 of the PKI domain is positioned between the A-site finger (nt 1008–1043 of 25S rRNA) and the P site of the 60S subunit, comprising helix 84 of 25S rRNA (nt.	RESULTS
64	77	A-site finger	structure_element	In Structure I, SL3 of the PKI domain is positioned between the A-site finger (nt 1008–1043 of 25S rRNA) and the P site of the 60S subunit, comprising helix 84 of 25S rRNA (nt.	RESULTS
82	91	1008–1043	residue_range	In Structure I, SL3 of the PKI domain is positioned between the A-site finger (nt 1008–1043 of 25S rRNA) and the P site of the 60S subunit, comprising helix 84 of 25S rRNA (nt.	RESULTS
95	103	25S rRNA	chemical	In Structure I, SL3 of the PKI domain is positioned between the A-site finger (nt 1008–1043 of 25S rRNA) and the P site of the 60S subunit, comprising helix 84 of 25S rRNA (nt.	RESULTS
113	119	P site	site	In Structure I, SL3 of the PKI domain is positioned between the A-site finger (nt 1008–1043 of 25S rRNA) and the P site of the 60S subunit, comprising helix 84 of 25S rRNA (nt.	RESULTS
127	130	60S	complex_assembly	In Structure I, SL3 of the PKI domain is positioned between the A-site finger (nt 1008–1043 of 25S rRNA) and the P site of the 60S subunit, comprising helix 84 of 25S rRNA (nt.	RESULTS
131	138	subunit	structure_element	In Structure I, SL3 of the PKI domain is positioned between the A-site finger (nt 1008–1043 of 25S rRNA) and the P site of the 60S subunit, comprising helix 84 of 25S rRNA (nt.	RESULTS
151	159	helix 84	structure_element	In Structure I, SL3 of the PKI domain is positioned between the A-site finger (nt 1008–1043 of 25S rRNA) and the P site of the 60S subunit, comprising helix 84 of 25S rRNA (nt.	RESULTS
163	171	25S rRNA	chemical	In Structure I, SL3 of the PKI domain is positioned between the A-site finger (nt 1008–1043 of 25S rRNA) and the P site of the 60S subunit, comprising helix 84 of 25S rRNA (nt.	RESULTS
0	9	2668–2687	residue_range	2668–2687) and protein uL5 (Figure 3—figure supplement 6).	RESULTS
23	26	uL5	protein	2668–2687) and protein uL5 (Figure 3—figure supplement 6).	RESULTS
17	20	SL3	structure_element	This position of SL3 is ~25 Å away from that in the 80S•IRES initiation state, in which PKI and SL3 closely mimic the ASL and elbow of the A-site tRNA, respectively.	RESULTS
52	60	80S•IRES	complex_assembly	This position of SL3 is ~25 Å away from that in the 80S•IRES initiation state, in which PKI and SL3 closely mimic the ASL and elbow of the A-site tRNA, respectively.	RESULTS
61	71	initiation	protein_state	This position of SL3 is ~25 Å away from that in the 80S•IRES initiation state, in which PKI and SL3 closely mimic the ASL and elbow of the A-site tRNA, respectively.	RESULTS
88	91	PKI	structure_element	This position of SL3 is ~25 Å away from that in the 80S•IRES initiation state, in which PKI and SL3 closely mimic the ASL and elbow of the A-site tRNA, respectively.	RESULTS
96	99	SL3	structure_element	This position of SL3 is ~25 Å away from that in the 80S•IRES initiation state, in which PKI and SL3 closely mimic the ASL and elbow of the A-site tRNA, respectively.	RESULTS
118	121	ASL	structure_element	This position of SL3 is ~25 Å away from that in the 80S•IRES initiation state, in which PKI and SL3 closely mimic the ASL and elbow of the A-site tRNA, respectively.	RESULTS
126	131	elbow	structure_element	This position of SL3 is ~25 Å away from that in the 80S•IRES initiation state, in which PKI and SL3 closely mimic the ASL and elbow of the A-site tRNA, respectively.	RESULTS
139	145	A-site	site	This position of SL3 is ~25 Å away from that in the 80S•IRES initiation state, in which PKI and SL3 closely mimic the ASL and elbow of the A-site tRNA, respectively.	RESULTS
146	150	tRNA	chemical	This position of SL3 is ~25 Å away from that in the 80S•IRES initiation state, in which PKI and SL3 closely mimic the ASL and elbow of the A-site tRNA, respectively.	RESULTS
33	43	initiation	protein_state	As such, the transition from the initiation state to Structure I involves repositioning of SL3 around the A-site finger, resembling the transition between the pre-translocation A/P and A/P* tRNA.	RESULTS
53	64	Structure I	evidence	As such, the transition from the initiation state to Structure I involves repositioning of SL3 around the A-site finger, resembling the transition between the pre-translocation A/P and A/P* tRNA.	RESULTS
91	94	SL3	structure_element	As such, the transition from the initiation state to Structure I involves repositioning of SL3 around the A-site finger, resembling the transition between the pre-translocation A/P and A/P* tRNA.	RESULTS
106	119	A-site finger	structure_element	As such, the transition from the initiation state to Structure I involves repositioning of SL3 around the A-site finger, resembling the transition between the pre-translocation A/P and A/P* tRNA.	RESULTS
159	176	pre-translocation	protein_state	As such, the transition from the initiation state to Structure I involves repositioning of SL3 around the A-site finger, resembling the transition between the pre-translocation A/P and A/P* tRNA.	RESULTS
177	180	A/P	site	As such, the transition from the initiation state to Structure I involves repositioning of SL3 around the A-site finger, resembling the transition between the pre-translocation A/P and A/P* tRNA.	RESULTS
185	189	A/P*	site	As such, the transition from the initiation state to Structure I involves repositioning of SL3 around the A-site finger, resembling the transition between the pre-translocation A/P and A/P* tRNA.	RESULTS
190	194	tRNA	chemical	As such, the transition from the initiation state to Structure I involves repositioning of SL3 around the A-site finger, resembling the transition between the pre-translocation A/P and A/P* tRNA.	RESULTS
71	84	P site region	site	The second set of major structural changes involves interaction of the P site region of the large subunit with the hinge point of the IRES bending between the 5´ domain and the PKI domain (nt. 6886–6890).	RESULTS
92	105	large subunit	structure_element	The second set of major structural changes involves interaction of the P site region of the large subunit with the hinge point of the IRES bending between the 5´ domain and the PKI domain (nt. 6886–6890).	RESULTS
115	126	hinge point	structure_element	The second set of major structural changes involves interaction of the P site region of the large subunit with the hinge point of the IRES bending between the 5´ domain and the PKI domain (nt. 6886–6890).	RESULTS
134	138	IRES	site	The second set of major structural changes involves interaction of the P site region of the large subunit with the hinge point of the IRES bending between the 5´ domain and the PKI domain (nt. 6886–6890).	RESULTS
159	168	5´ domain	structure_element	The second set of major structural changes involves interaction of the P site region of the large subunit with the hinge point of the IRES bending between the 5´ domain and the PKI domain (nt. 6886–6890).	RESULTS
177	180	PKI	structure_element	The second set of major structural changes involves interaction of the P site region of the large subunit with the hinge point of the IRES bending between the 5´ domain and the PKI domain (nt. 6886–6890).	RESULTS
193	202	6886–6890	residue_range	The second set of major structural changes involves interaction of the P site region of the large subunit with the hinge point of the IRES bending between the 5´ domain and the PKI domain (nt. 6886–6890).	RESULTS
7	18	highly bent	protein_state	In the highly bent Structures III and IV, the hinge region interacts with the universally conserved uL5 and the C-terminal tail of eL42 (Figure 3—figure supplement 7).	RESULTS
19	40	Structures III and IV	evidence	In the highly bent Structures III and IV, the hinge region interacts with the universally conserved uL5 and the C-terminal tail of eL42 (Figure 3—figure supplement 7).	RESULTS
46	58	hinge region	structure_element	In the highly bent Structures III and IV, the hinge region interacts with the universally conserved uL5 and the C-terminal tail of eL42 (Figure 3—figure supplement 7).	RESULTS
78	99	universally conserved	protein_state	In the highly bent Structures III and IV, the hinge region interacts with the universally conserved uL5 and the C-terminal tail of eL42 (Figure 3—figure supplement 7).	RESULTS
100	103	uL5	protein	In the highly bent Structures III and IV, the hinge region interacts with the universally conserved uL5 and the C-terminal tail of eL42 (Figure 3—figure supplement 7).	RESULTS
112	127	C-terminal tail	structure_element	In the highly bent Structures III and IV, the hinge region interacts with the universally conserved uL5 and the C-terminal tail of eL42 (Figure 3—figure supplement 7).	RESULTS
131	135	eL42	protein	In the highly bent Structures III and IV, the hinge region interacts with the universally conserved uL5 and the C-terminal tail of eL42 (Figure 3—figure supplement 7).	RESULTS
16	24	extended	protein_state	However, in the extended conformations, these parts of the IRES and the 60S subunit are separated by more than 10 Å, suggesting that an interaction between them stabilizes the bent conformations but not the extended ones.	RESULTS
59	63	IRES	site	However, in the extended conformations, these parts of the IRES and the 60S subunit are separated by more than 10 Å, suggesting that an interaction between them stabilizes the bent conformations but not the extended ones.	RESULTS
72	75	60S	complex_assembly	However, in the extended conformations, these parts of the IRES and the 60S subunit are separated by more than 10 Å, suggesting that an interaction between them stabilizes the bent conformations but not the extended ones.	RESULTS
76	83	subunit	structure_element	However, in the extended conformations, these parts of the IRES and the 60S subunit are separated by more than 10 Å, suggesting that an interaction between them stabilizes the bent conformations but not the extended ones.	RESULTS
176	180	bent	protein_state	However, in the extended conformations, these parts of the IRES and the 60S subunit are separated by more than 10 Å, suggesting that an interaction between them stabilizes the bent conformations but not the extended ones.	RESULTS
207	215	extended	protein_state	However, in the extended conformations, these parts of the IRES and the 60S subunit are separated by more than 10 Å, suggesting that an interaction between them stabilizes the bent conformations but not the extended ones.	RESULTS
37	43	loop 3	structure_element	Another local rearrangement concerns loop 3, also known as the variable loop region , which connects the ASL- and mRNA-like parts of PKI.	RESULTS
63	83	variable loop region	structure_element	Another local rearrangement concerns loop 3, also known as the variable loop region , which connects the ASL- and mRNA-like parts of PKI.	RESULTS
105	129	ASL- and mRNA-like parts	structure_element	Another local rearrangement concerns loop 3, also known as the variable loop region , which connects the ASL- and mRNA-like parts of PKI.	RESULTS
133	136	PKI	structure_element	Another local rearrangement concerns loop 3, also known as the variable loop region , which connects the ASL- and mRNA-like parts of PKI.	RESULTS
5	9	loop	structure_element	This loop is poorly resolved in Structures I through IV, suggesting conformational flexibility in agreement with structural studies of the isolated PKI and biochemical studies of unbound IRESs.	RESULTS
32	55	Structures I through IV	evidence	This loop is poorly resolved in Structures I through IV, suggesting conformational flexibility in agreement with structural studies of the isolated PKI and biochemical studies of unbound IRESs.	RESULTS
113	131	structural studies	experimental_method	This loop is poorly resolved in Structures I through IV, suggesting conformational flexibility in agreement with structural studies of the isolated PKI and biochemical studies of unbound IRESs.	RESULTS
139	147	isolated	protein_state	This loop is poorly resolved in Structures I through IV, suggesting conformational flexibility in agreement with structural studies of the isolated PKI and biochemical studies of unbound IRESs.	RESULTS
148	151	PKI	structure_element	This loop is poorly resolved in Structures I through IV, suggesting conformational flexibility in agreement with structural studies of the isolated PKI and biochemical studies of unbound IRESs.	RESULTS
156	175	biochemical studies	experimental_method	This loop is poorly resolved in Structures I through IV, suggesting conformational flexibility in agreement with structural studies of the isolated PKI and biochemical studies of unbound IRESs.	RESULTS
179	186	unbound	protein_state	This loop is poorly resolved in Structures I through IV, suggesting conformational flexibility in agreement with structural studies of the isolated PKI and biochemical studies of unbound IRESs.	RESULTS
187	192	IRESs	site	This loop is poorly resolved in Structures I through IV, suggesting conformational flexibility in agreement with structural studies of the isolated PKI and biochemical studies of unbound IRESs.	RESULTS
3	14	Structure V	evidence	In Structure V, loop 3 is bound in the 40S E site and the backbone of loop 3 near the codon-like part of PKI (at nt.	RESULTS
16	22	loop 3	structure_element	In Structure V, loop 3 is bound in the 40S E site and the backbone of loop 3 near the codon-like part of PKI (at nt.	RESULTS
26	34	bound in	protein_state	In Structure V, loop 3 is bound in the 40S E site and the backbone of loop 3 near the codon-like part of PKI (at nt.	RESULTS
39	42	40S	complex_assembly	In Structure V, loop 3 is bound in the 40S E site and the backbone of loop 3 near the codon-like part of PKI (at nt.	RESULTS
43	49	E site	site	In Structure V, loop 3 is bound in the 40S E site and the backbone of loop 3 near the codon-like part of PKI (at nt.	RESULTS
70	76	loop 3	structure_element	In Structure V, loop 3 is bound in the 40S E site and the backbone of loop 3 near the codon-like part of PKI (at nt.	RESULTS
86	101	codon-like part	structure_element	In Structure V, loop 3 is bound in the 40S E site and the backbone of loop 3 near the codon-like part of PKI (at nt.	RESULTS
105	108	PKI	structure_element	In Structure V, loop 3 is bound in the 40S E site and the backbone of loop 3 near the codon-like part of PKI (at nt.	RESULTS
0	9	6945–6946	residue_range	6945–6946) interacts with R148 and R157 in β-hairpin of uS7.	RESULTS
26	30	R148	residue_name_number	6945–6946) interacts with R148 and R157 in β-hairpin of uS7.	RESULTS
35	39	R157	residue_name_number	6945–6946) interacts with R148 and R157 in β-hairpin of uS7.	RESULTS
43	52	β-hairpin	structure_element	6945–6946) interacts with R148 and R157 in β-hairpin of uS7.	RESULTS
56	59	uS7	protein	6945–6946) interacts with R148 and R157 in β-hairpin of uS7.	RESULTS
19	25	loop 3	structure_element	The interaction of loop 3 backbone with uS7 resembles that of the anticodon-stem loop of E-site tRNA in the post-translocation 80S•2tRNA•mRNA structure (Figure 3—figure supplement 5).	RESULTS
40	43	uS7	protein	The interaction of loop 3 backbone with uS7 resembles that of the anticodon-stem loop of E-site tRNA in the post-translocation 80S•2tRNA•mRNA structure (Figure 3—figure supplement 5).	RESULTS
66	85	anticodon-stem loop	structure_element	The interaction of loop 3 backbone with uS7 resembles that of the anticodon-stem loop of E-site tRNA in the post-translocation 80S•2tRNA•mRNA structure (Figure 3—figure supplement 5).	RESULTS
89	95	E-site	site	The interaction of loop 3 backbone with uS7 resembles that of the anticodon-stem loop of E-site tRNA in the post-translocation 80S•2tRNA•mRNA structure (Figure 3—figure supplement 5).	RESULTS
96	100	tRNA	chemical	The interaction of loop 3 backbone with uS7 resembles that of the anticodon-stem loop of E-site tRNA in the post-translocation 80S•2tRNA•mRNA structure (Figure 3—figure supplement 5).	RESULTS
108	126	post-translocation	protein_state	The interaction of loop 3 backbone with uS7 resembles that of the anticodon-stem loop of E-site tRNA in the post-translocation 80S•2tRNA•mRNA structure (Figure 3—figure supplement 5).	RESULTS
127	141	80S•2tRNA•mRNA	complex_assembly	The interaction of loop 3 backbone with uS7 resembles that of the anticodon-stem loop of E-site tRNA in the post-translocation 80S•2tRNA•mRNA structure (Figure 3—figure supplement 5).	RESULTS
142	151	structure	evidence	The interaction of loop 3 backbone with uS7 resembles that of the anticodon-stem loop of E-site tRNA in the post-translocation 80S•2tRNA•mRNA structure (Figure 3—figure supplement 5).	RESULTS
12	18	loop 3	structure_element	Ordering of loop 3 suggests that this flexible region contributes to the stabilization of the PKI domain in the post-translocation state.	RESULTS
94	97	PKI	structure_element	Ordering of loop 3 suggests that this flexible region contributes to the stabilization of the PKI domain in the post-translocation state.	RESULTS
112	130	post-translocation	protein_state	Ordering of loop 3 suggests that this flexible region contributes to the stabilization of the PKI domain in the post-translocation state.	RESULTS
82	88	loop 3	structure_element	This interpretation is consistent with the recent observation that alterations in loop 3 of the CrPV IRES result in decreased efficiency of translocation.	RESULTS
96	100	CrPV	species	This interpretation is consistent with the recent observation that alterations in loop 3 of the CrPV IRES result in decreased efficiency of translocation.	RESULTS
101	105	IRES	site	This interpretation is consistent with the recent observation that alterations in loop 3 of the CrPV IRES result in decreased efficiency of translocation.	RESULTS
0	4	eEF2	protein	eEF2 structures	RESULTS
5	15	structures	evidence	eEF2 structures	RESULTS
16	28	80S ribosome	complex_assembly	Elements of the 80S ribosome that contact eEF2 in Structures I through V.	FIG
42	46	eEF2	protein	Elements of the 80S ribosome that contact eEF2 in Structures I through V.	FIG
50	72	Structures I through V	evidence	Elements of the 80S ribosome that contact eEF2 in Structures I through V.	FIG
41	45	eEF2	protein	The view and colors are as in Figure 5b: eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
65	69	IRES	site	The view and colors are as in Figure 5b: eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
70	73	RNA	chemical	The view and colors are as in Figure 5b: eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
82	85	40S	complex_assembly	The view and colors are as in Figure 5b: eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
86	93	subunit	structure_element	The view and colors are as in Figure 5b: eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
86	93	subunit	structure_element	The view and colors are as in Figure 5b: eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
114	117	60S	complex_assembly	The view and colors are as in Figure 5b: eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
0	7	Cryo-EM	experimental_method	Cryo-EM density of the GTPase region in Structures I and II.	FIG
8	15	density	evidence	Cryo-EM density of the GTPase region in Structures I and II.	FIG
23	36	GTPase region	structure_element	Cryo-EM density of the GTPase region in Structures I and II.	FIG
40	59	Structures I and II	evidence	Cryo-EM density of the GTPase region in Structures I and II.	FIG
4	17	switch loop I	structure_element	The switch loop I in Structure I is shown in blue.	FIG
21	32	Structure I	evidence	The switch loop I in Structure I is shown in blue.	FIG
29	42	switch loop I	structure_element	The putative position of the switch loop I, unresolved in the density of Structure II, is shown with a dashed line.	FIG
62	69	density	evidence	The putative position of the switch loop I, unresolved in the density of Structure II, is shown with a dashed line.	FIG
73	85	Structure II	evidence	The putative position of the switch loop I, unresolved in the density of Structure II, is shown with a dashed line.	FIG
15	23	ribosome	complex_assembly	Colors for the ribosome and eEF2 are as in Figure 1.	FIG
28	32	eEF2	protein	Colors for the ribosome and eEF2 are as in Figure 1.	FIG
34	38	eEF2	protein	Conformations and interactions of eEF2.	FIG
21	25	eEF2	protein	(a) Conformations of eEF2 in Structures I-V and domain organization of eEF2 are shown.	FIG
29	43	Structures I-V	evidence	(a) Conformations of eEF2 in Structures I-V and domain organization of eEF2 are shown.	FIG
71	75	eEF2	protein	(a) Conformations of eEF2 in Structures I-V and domain organization of eEF2 are shown.	FIG
22	26	eEF2	protein	Roman numerals denote eEF2 domains.	FIG
0	13	Superposition	experimental_method	Superposition was obtained by structural alignment of domains I and II.	FIG
30	50	structural alignment	experimental_method	Superposition was obtained by structural alignment of domains I and II.	FIG
62	63	I	structure_element	Superposition was obtained by structural alignment of domains I and II.	FIG
68	70	II	structure_element	Superposition was obtained by structural alignment of domains I and II.	FIG
20	32	80S ribosome	complex_assembly	(b) Elements of the 80S ribosome in Structures I and V that contact eEF2.	FIG
36	54	Structures I and V	evidence	(b) Elements of the 80S ribosome in Structures I and V that contact eEF2.	FIG
68	72	eEF2	protein	(b) Elements of the 80S ribosome in Structures I and V that contact eEF2.	FIG
0	4	eEF2	protein	eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
24	28	IRES	site	eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
29	32	RNA	chemical	eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
41	44	40S	complex_assembly	eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
45	52	subunit	structure_element	eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
73	76	60S	complex_assembly	eEF2 is shown in green, IRES RNA in red, 40S subunit elements in orange, 60S in cyan/teal.	FIG
35	48	eEF2•sordarin	complex_assembly	(c) Comparison of conformations of eEF2•sordarin in Structure I (light green) with those of free apo-eEF2 (magenta) and eEF2•sordarin (teal).	FIG
52	63	Structure I	evidence	(c) Comparison of conformations of eEF2•sordarin in Structure I (light green) with those of free apo-eEF2 (magenta) and eEF2•sordarin (teal).	FIG
92	96	free	protein_state	(c) Comparison of conformations of eEF2•sordarin in Structure I (light green) with those of free apo-eEF2 (magenta) and eEF2•sordarin (teal).	FIG
97	100	apo	protein_state	(c) Comparison of conformations of eEF2•sordarin in Structure I (light green) with those of free apo-eEF2 (magenta) and eEF2•sordarin (teal).	FIG
101	105	eEF2	protein	(c) Comparison of conformations of eEF2•sordarin in Structure I (light green) with those of free apo-eEF2 (magenta) and eEF2•sordarin (teal).	FIG
120	133	eEF2•sordarin	complex_assembly	(c) Comparison of conformations of eEF2•sordarin in Structure I (light green) with those of free apo-eEF2 (magenta) and eEF2•sordarin (teal).	FIG
24	38	GTPase domains	structure_element	(d) Interactions of the GTPase domains with the 40S and 60S subunits in Structure I (colored in green/blue, eEF2; orange, 40S; cyan/teal, 60S) and in Structure II (gray).	FIG
48	51	40S	complex_assembly	(d) Interactions of the GTPase domains with the 40S and 60S subunits in Structure I (colored in green/blue, eEF2; orange, 40S; cyan/teal, 60S) and in Structure II (gray).	FIG
56	59	60S	complex_assembly	(d) Interactions of the GTPase domains with the 40S and 60S subunits in Structure I (colored in green/blue, eEF2; orange, 40S; cyan/teal, 60S) and in Structure II (gray).	FIG
60	68	subunits	structure_element	(d) Interactions of the GTPase domains with the 40S and 60S subunits in Structure I (colored in green/blue, eEF2; orange, 40S; cyan/teal, 60S) and in Structure II (gray).	FIG
72	83	Structure I	evidence	(d) Interactions of the GTPase domains with the 40S and 60S subunits in Structure I (colored in green/blue, eEF2; orange, 40S; cyan/teal, 60S) and in Structure II (gray).	FIG
108	112	eEF2	protein	(d) Interactions of the GTPase domains with the 40S and 60S subunits in Structure I (colored in green/blue, eEF2; orange, 40S; cyan/teal, 60S) and in Structure II (gray).	FIG
122	125	40S	complex_assembly	(d) Interactions of the GTPase domains with the 40S and 60S subunits in Structure I (colored in green/blue, eEF2; orange, 40S; cyan/teal, 60S) and in Structure II (gray).	FIG
138	141	60S	complex_assembly	(d) Interactions of the GTPase domains with the 40S and 60S subunits in Structure I (colored in green/blue, eEF2; orange, 40S; cyan/teal, 60S) and in Structure II (gray).	FIG
150	162	Structure II	evidence	(d) Interactions of the GTPase domains with the 40S and 60S subunits in Structure I (colored in green/blue, eEF2; orange, 40S; cyan/teal, 60S) and in Structure II (gray).	FIG
0	13	Switch loop I	structure_element	Switch loop I (SWI) in Structure I is in blue; dashed line shows the putative location of unresolved switch loop I in Structure II.	FIG
15	18	SWI	structure_element	Switch loop I (SWI) in Structure I is in blue; dashed line shows the putative location of unresolved switch loop I in Structure II.	FIG
23	34	Structure I	evidence	Switch loop I (SWI) in Structure I is in blue; dashed line shows the putative location of unresolved switch loop I in Structure II.	FIG
101	114	switch loop I	structure_element	Switch loop I (SWI) in Structure I is in blue; dashed line shows the putative location of unresolved switch loop I in Structure II.	FIG
118	130	Structure II	evidence	Switch loop I (SWI) in Structure I is in blue; dashed line shows the putative location of unresolved switch loop I in Structure II.	FIG
0	13	Superposition	experimental_method	Superposition was obtained by structural alignment of the 25S rRNAs.	FIG
30	50	structural alignment	experimental_method	Superposition was obtained by structural alignment of the 25S rRNAs.	FIG
58	67	25S rRNAs	chemical	Superposition was obtained by structural alignment of the 25S rRNAs.	FIG
22	30	GTP-like	protein_state	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
47	55	eEF2•GDP	complex_assembly	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
59	70	Structure I	evidence	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
99	108	70S-bound	protein_state	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
109	127	elongation factors	protein_type	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
128	139	EF-Tu•GDPCP	complex_assembly	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
151	172	EF-G•GDP•fusidic acid	complex_assembly	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
212	219	Cryo-EM	experimental_method	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
220	227	density	evidence	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
236	257	guanosine diphosphate	chemical	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
258	266	bound in	protein_state	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
271	284	GTPase center	site	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
305	322	sarcin-ricin loop	structure_element	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
326	334	25S rRNA	chemical	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
345	357	Structure II	evidence	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
381	403	sordarin-binding sites	site	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
411	425	ribosome-bound	protein_state	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
440	452	Structure II	evidence	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
467	471	eEF2	protein	(e) Comparison of the GTP-like conformation of eEF2•GDP in Structure I (light green) with those of 70S-bound elongation factors EF-Tu•GDPCP (teal) and EF-G•GDP•fusidic acid (magenta; fusidic acid not shown). (f) Cryo-EM density showing guanosine diphosphate bound in the GTPase center (green) next to the sarcin-ricin loop of 25S rRNA (cyan) of Structure II. (g) Comparison of the sordarin-binding sites in the ribosome-bound (light green; Structure II) and isolated eEF2 (teal).	FIG
4	11	Cryo-EM	experimental_method	(h) Cryo-EM density showing the sordarin-binding pocket of eEF2 (Structure II).	FIG
12	19	density	evidence	(h) Cryo-EM density showing the sordarin-binding pocket of eEF2 (Structure II).	FIG
32	55	sordarin-binding pocket	site	(h) Cryo-EM density showing the sordarin-binding pocket of eEF2 (Structure II).	FIG
59	63	eEF2	protein	(h) Cryo-EM density showing the sordarin-binding pocket of eEF2 (Structure II).	FIG
65	77	Structure II	evidence	(h) Cryo-EM density showing the sordarin-binding pocket of eEF2 (Structure II).	FIG
0	8	Sordarin	chemical	Sordarin is shown in pink with oxygen atoms in red.	FIG
0	17	Elongation factor	protein_type	Elongation factor eEF2 in all five structures is bound with GDP and sordarin (Figure 5).	RESULTS
18	22	eEF2	protein	Elongation factor eEF2 in all five structures is bound with GDP and sordarin (Figure 5).	RESULTS
35	45	structures	evidence	Elongation factor eEF2 in all five structures is bound with GDP and sordarin (Figure 5).	RESULTS
49	59	bound with	protein_state	Elongation factor eEF2 in all five structures is bound with GDP and sordarin (Figure 5).	RESULTS
60	63	GDP	chemical	Elongation factor eEF2 in all five structures is bound with GDP and sordarin (Figure 5).	RESULTS
68	76	sordarin	chemical	Elongation factor eEF2 in all five structures is bound with GDP and sordarin (Figure 5).	RESULTS
4	21	elongation factor	protein_type	The elongation factor consists of three dynamic superdomains: an N-terminal globular superdomain formed by the G (GTPase) domain (domain I) and domain II; a linker domain III; and a C-terminal superdomain comprising domains IV and V (Figure 5a).	RESULTS
48	60	superdomains	structure_element	The elongation factor consists of three dynamic superdomains: an N-terminal globular superdomain formed by the G (GTPase) domain (domain I) and domain II; a linker domain III; and a C-terminal superdomain comprising domains IV and V (Figure 5a).	RESULTS
85	96	superdomain	structure_element	The elongation factor consists of three dynamic superdomains: an N-terminal globular superdomain formed by the G (GTPase) domain (domain I) and domain II; a linker domain III; and a C-terminal superdomain comprising domains IV and V (Figure 5a).	RESULTS
111	128	G (GTPase) domain	structure_element	The elongation factor consists of three dynamic superdomains: an N-terminal globular superdomain formed by the G (GTPase) domain (domain I) and domain II; a linker domain III; and a C-terminal superdomain comprising domains IV and V (Figure 5a).	RESULTS
137	138	I	structure_element	The elongation factor consists of three dynamic superdomains: an N-terminal globular superdomain formed by the G (GTPase) domain (domain I) and domain II; a linker domain III; and a C-terminal superdomain comprising domains IV and V (Figure 5a).	RESULTS
151	153	II	structure_element	The elongation factor consists of three dynamic superdomains: an N-terminal globular superdomain formed by the G (GTPase) domain (domain I) and domain II; a linker domain III; and a C-terminal superdomain comprising domains IV and V (Figure 5a).	RESULTS
157	174	linker domain III	structure_element	The elongation factor consists of three dynamic superdomains: an N-terminal globular superdomain formed by the G (GTPase) domain (domain I) and domain II; a linker domain III; and a C-terminal superdomain comprising domains IV and V (Figure 5a).	RESULTS
193	204	superdomain	structure_element	The elongation factor consists of three dynamic superdomains: an N-terminal globular superdomain formed by the G (GTPase) domain (domain I) and domain II; a linker domain III; and a C-terminal superdomain comprising domains IV and V (Figure 5a).	RESULTS
224	226	IV	structure_element	The elongation factor consists of three dynamic superdomains: an N-terminal globular superdomain formed by the G (GTPase) domain (domain I) and domain II; a linker domain III; and a C-terminal superdomain comprising domains IV and V (Figure 5a).	RESULTS
231	232	V	structure_element	The elongation factor consists of three dynamic superdomains: an N-terminal globular superdomain formed by the G (GTPase) domain (domain I) and domain II; a linker domain III; and a C-terminal superdomain comprising domains IV and V (Figure 5a).	RESULTS
7	9	IV	structure_element	Domain IV extends from the main body and is critical for translocation catalyzed by eEF2 or EF-G. ADP-ribosylation of eEF2 at the tip of domain IV or deletion of domain IV from EF-G abrogate translocation.	RESULTS
32	36	body	structure_element	Domain IV extends from the main body and is critical for translocation catalyzed by eEF2 or EF-G. ADP-ribosylation of eEF2 at the tip of domain IV or deletion of domain IV from EF-G abrogate translocation.	RESULTS
84	88	eEF2	protein	Domain IV extends from the main body and is critical for translocation catalyzed by eEF2 or EF-G. ADP-ribosylation of eEF2 at the tip of domain IV or deletion of domain IV from EF-G abrogate translocation.	RESULTS
92	96	EF-G	protein	Domain IV extends from the main body and is critical for translocation catalyzed by eEF2 or EF-G. ADP-ribosylation of eEF2 at the tip of domain IV or deletion of domain IV from EF-G abrogate translocation.	RESULTS
98	114	ADP-ribosylation	ptm	Domain IV extends from the main body and is critical for translocation catalyzed by eEF2 or EF-G. ADP-ribosylation of eEF2 at the tip of domain IV or deletion of domain IV from EF-G abrogate translocation.	RESULTS
118	122	eEF2	protein	Domain IV extends from the main body and is critical for translocation catalyzed by eEF2 or EF-G. ADP-ribosylation of eEF2 at the tip of domain IV or deletion of domain IV from EF-G abrogate translocation.	RESULTS
144	146	IV	structure_element	Domain IV extends from the main body and is critical for translocation catalyzed by eEF2 or EF-G. ADP-ribosylation of eEF2 at the tip of domain IV or deletion of domain IV from EF-G abrogate translocation.	RESULTS
150	158	deletion	experimental_method	Domain IV extends from the main body and is critical for translocation catalyzed by eEF2 or EF-G. ADP-ribosylation of eEF2 at the tip of domain IV or deletion of domain IV from EF-G abrogate translocation.	RESULTS
169	171	IV	structure_element	Domain IV extends from the main body and is critical for translocation catalyzed by eEF2 or EF-G. ADP-ribosylation of eEF2 at the tip of domain IV or deletion of domain IV from EF-G abrogate translocation.	RESULTS
177	181	EF-G	protein	Domain IV extends from the main body and is critical for translocation catalyzed by eEF2 or EF-G. ADP-ribosylation of eEF2 at the tip of domain IV or deletion of domain IV from EF-G abrogate translocation.	RESULTS
3	21	post-translocation	protein_state	In post-translocation-like 80S•tRNA•eEF2 complexes, domain IV binds in the 40S A site, suggesting direct involvement of domain IV in translocation of tRNA from the A to P site.	RESULTS
27	40	80S•tRNA•eEF2	complex_assembly	In post-translocation-like 80S•tRNA•eEF2 complexes, domain IV binds in the 40S A site, suggesting direct involvement of domain IV in translocation of tRNA from the A to P site.	RESULTS
59	61	IV	structure_element	In post-translocation-like 80S•tRNA•eEF2 complexes, domain IV binds in the 40S A site, suggesting direct involvement of domain IV in translocation of tRNA from the A to P site.	RESULTS
75	78	40S	complex_assembly	In post-translocation-like 80S•tRNA•eEF2 complexes, domain IV binds in the 40S A site, suggesting direct involvement of domain IV in translocation of tRNA from the A to P site.	RESULTS
79	85	A site	site	In post-translocation-like 80S•tRNA•eEF2 complexes, domain IV binds in the 40S A site, suggesting direct involvement of domain IV in translocation of tRNA from the A to P site.	RESULTS
127	129	IV	structure_element	In post-translocation-like 80S•tRNA•eEF2 complexes, domain IV binds in the 40S A site, suggesting direct involvement of domain IV in translocation of tRNA from the A to P site.	RESULTS
150	154	tRNA	chemical	In post-translocation-like 80S•tRNA•eEF2 complexes, domain IV binds in the 40S A site, suggesting direct involvement of domain IV in translocation of tRNA from the A to P site.	RESULTS
164	175	A to P site	site	In post-translocation-like 80S•tRNA•eEF2 complexes, domain IV binds in the 40S A site, suggesting direct involvement of domain IV in translocation of tRNA from the A to P site.	RESULTS
0	3	GDP	chemical	GDP in our structures is bound in the GTPase center (Figures 5d, e and f) and sordarin is sandwiched between the β-platforms of domains III and V (Figures 5g and h), as in the structure of free eEF2•sordarin complex.	RESULTS
11	21	structures	evidence	GDP in our structures is bound in the GTPase center (Figures 5d, e and f) and sordarin is sandwiched between the β-platforms of domains III and V (Figures 5g and h), as in the structure of free eEF2•sordarin complex.	RESULTS
25	33	bound in	protein_state	GDP in our structures is bound in the GTPase center (Figures 5d, e and f) and sordarin is sandwiched between the β-platforms of domains III and V (Figures 5g and h), as in the structure of free eEF2•sordarin complex.	RESULTS
38	51	GTPase center	site	GDP in our structures is bound in the GTPase center (Figures 5d, e and f) and sordarin is sandwiched between the β-platforms of domains III and V (Figures 5g and h), as in the structure of free eEF2•sordarin complex.	RESULTS
78	86	sordarin	chemical	GDP in our structures is bound in the GTPase center (Figures 5d, e and f) and sordarin is sandwiched between the β-platforms of domains III and V (Figures 5g and h), as in the structure of free eEF2•sordarin complex.	RESULTS
113	124	β-platforms	structure_element	GDP in our structures is bound in the GTPase center (Figures 5d, e and f) and sordarin is sandwiched between the β-platforms of domains III and V (Figures 5g and h), as in the structure of free eEF2•sordarin complex.	RESULTS
136	139	III	structure_element	GDP in our structures is bound in the GTPase center (Figures 5d, e and f) and sordarin is sandwiched between the β-platforms of domains III and V (Figures 5g and h), as in the structure of free eEF2•sordarin complex.	RESULTS
144	145	V	structure_element	GDP in our structures is bound in the GTPase center (Figures 5d, e and f) and sordarin is sandwiched between the β-platforms of domains III and V (Figures 5g and h), as in the structure of free eEF2•sordarin complex.	RESULTS
176	185	structure	evidence	GDP in our structures is bound in the GTPase center (Figures 5d, e and f) and sordarin is sandwiched between the β-platforms of domains III and V (Figures 5g and h), as in the structure of free eEF2•sordarin complex.	RESULTS
189	193	free	protein_state	GDP in our structures is bound in the GTPase center (Figures 5d, e and f) and sordarin is sandwiched between the β-platforms of domains III and V (Figures 5g and h), as in the structure of free eEF2•sordarin complex.	RESULTS
194	207	eEF2•sordarin	complex_assembly	GDP in our structures is bound in the GTPase center (Figures 5d, e and f) and sordarin is sandwiched between the β-platforms of domains III and V (Figures 5g and h), as in the structure of free eEF2•sordarin complex.	RESULTS
28	32	eEF2	protein	The global conformations of eEF2 (Figure 5a) are similar in these structures (all-atom RMSD ≤ 2 Å), but the positions of eEF2 relative to the 40S subunit differ substantially as a result of 40S subunit rotation (Figure 2—source data 1).	RESULTS
66	76	structures	evidence	The global conformations of eEF2 (Figure 5a) are similar in these structures (all-atom RMSD ≤ 2 Å), but the positions of eEF2 relative to the 40S subunit differ substantially as a result of 40S subunit rotation (Figure 2—source data 1).	RESULTS
87	91	RMSD	evidence	The global conformations of eEF2 (Figure 5a) are similar in these structures (all-atom RMSD ≤ 2 Å), but the positions of eEF2 relative to the 40S subunit differ substantially as a result of 40S subunit rotation (Figure 2—source data 1).	RESULTS
121	125	eEF2	protein	The global conformations of eEF2 (Figure 5a) are similar in these structures (all-atom RMSD ≤ 2 Å), but the positions of eEF2 relative to the 40S subunit differ substantially as a result of 40S subunit rotation (Figure 2—source data 1).	RESULTS
142	145	40S	complex_assembly	The global conformations of eEF2 (Figure 5a) are similar in these structures (all-atom RMSD ≤ 2 Å), but the positions of eEF2 relative to the 40S subunit differ substantially as a result of 40S subunit rotation (Figure 2—source data 1).	RESULTS
146	153	subunit	structure_element	The global conformations of eEF2 (Figure 5a) are similar in these structures (all-atom RMSD ≤ 2 Å), but the positions of eEF2 relative to the 40S subunit differ substantially as a result of 40S subunit rotation (Figure 2—source data 1).	RESULTS
190	193	40S	complex_assembly	The global conformations of eEF2 (Figure 5a) are similar in these structures (all-atom RMSD ≤ 2 Å), but the positions of eEF2 relative to the 40S subunit differ substantially as a result of 40S subunit rotation (Figure 2—source data 1).	RESULTS
194	201	subunit	structure_element	The global conformations of eEF2 (Figure 5a) are similar in these structures (all-atom RMSD ≤ 2 Å), but the positions of eEF2 relative to the 40S subunit differ substantially as a result of 40S subunit rotation (Figure 2—source data 1).	RESULTS
5	21	Structure I to V	evidence	From Structure I to V, eEF2 is rigidly attached to the GTPase-associated center of the 60S subunit.	RESULTS
23	27	eEF2	protein	From Structure I to V, eEF2 is rigidly attached to the GTPase-associated center of the 60S subunit.	RESULTS
55	79	GTPase-associated center	site	From Structure I to V, eEF2 is rigidly attached to the GTPase-associated center of the 60S subunit.	RESULTS
87	90	60S	complex_assembly	From Structure I to V, eEF2 is rigidly attached to the GTPase-associated center of the 60S subunit.	RESULTS
91	98	subunit	structure_element	From Structure I to V, eEF2 is rigidly attached to the GTPase-associated center of the 60S subunit.	RESULTS
4	28	GTPase-associated center	site	The GTPase-associated center comprises the P stalk (L11 and L7/L12 stalk in bacteria) and the sarcin-ricin loop (SRL, nt 3012–3042).	RESULTS
43	50	P stalk	structure_element	The GTPase-associated center comprises the P stalk (L11 and L7/L12 stalk in bacteria) and the sarcin-ricin loop (SRL, nt 3012–3042).	RESULTS
52	55	L11	structure_element	The GTPase-associated center comprises the P stalk (L11 and L7/L12 stalk in bacteria) and the sarcin-ricin loop (SRL, nt 3012–3042).	RESULTS
60	62	L7	structure_element	The GTPase-associated center comprises the P stalk (L11 and L7/L12 stalk in bacteria) and the sarcin-ricin loop (SRL, nt 3012–3042).	RESULTS
63	66	L12	structure_element	The GTPase-associated center comprises the P stalk (L11 and L7/L12 stalk in bacteria) and the sarcin-ricin loop (SRL, nt 3012–3042).	RESULTS
67	72	stalk	structure_element	The GTPase-associated center comprises the P stalk (L11 and L7/L12 stalk in bacteria) and the sarcin-ricin loop (SRL, nt 3012–3042).	RESULTS
76	84	bacteria	taxonomy_domain	The GTPase-associated center comprises the P stalk (L11 and L7/L12 stalk in bacteria) and the sarcin-ricin loop (SRL, nt 3012–3042).	RESULTS
94	111	sarcin-ricin loop	structure_element	The GTPase-associated center comprises the P stalk (L11 and L7/L12 stalk in bacteria) and the sarcin-ricin loop (SRL, nt 3012–3042).	RESULTS
113	116	SRL	structure_element	The GTPase-associated center comprises the P stalk (L11 and L7/L12 stalk in bacteria) and the sarcin-ricin loop (SRL, nt 3012–3042).	RESULTS
121	130	3012–3042	residue_range	The GTPase-associated center comprises the P stalk (L11 and L7/L12 stalk in bacteria) and the sarcin-ricin loop (SRL, nt 3012–3042).	RESULTS
12	20	25S rRNA	chemical	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
21	38	helices 43 and 44	structure_element	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
46	53	P stalk	structure_element	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
67	72	G1242	residue_name_number	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
77	82	A1270	residue_name_number	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
98	103	stack	bond_interaction	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
107	111	V754	residue_name_number	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
116	120	Y744	residue_name_number	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
131	132	V	structure_element	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
137	146	αββ motif	structure_element	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
154	163	eukaryote	taxonomy_domain	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
181	183	P0	protein	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
188	195	126–154	residue_range	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
230	244	long α-helix D	structure_element	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
249	256	172–188	residue_range	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
265	278	GTPase domain	structure_element	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
287	301	β-sheet region	structure_element	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
306	313	246–263	residue_range	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
322	342	GTPase domain insert	structure_element	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
347	356	G’ insert	structure_element	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
361	365	eEF2	protein	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
405	409	eEF2	protein	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
414	418	EF-G	protein	The tips of 25S rRNA helices 43 and 44 of the P stalk (nucleotides G1242 and A1270, respectively) stack on V754 and Y744 of domain V. An αββ motif of the eukaryote-specific protein P0 (aa 126–154) packs in the crevice between the long α-helix D (aa 172–188) of the GTPase domain and the β-sheet region (aa 246–263) of the GTPase domain insert (or G’ insert) of eEF2 (secondary-structure nomenclatures for eEF2 and EF-G are the same).	RESULTS
13	24	P/L11 stalk	structure_element	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
85	101	Structure I to V	evidence	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
112	140	root-mean-square differences	evidence	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
149	157	25S rRNA	chemical	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
165	172	P stalk	structure_element	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
177	186	1223–1286	residue_range	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
251	259	80S•IRES	complex_assembly	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
275	285	absence of	protein_state	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
286	290	eEF2	protein	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
302	316	80S•2tRNA•mRNA	complex_assembly	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
330	337	P stalk	structure_element	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
369	375	A site	site	Although the P/L11 stalk is known to be dynamic, its position remains unchanged from Structure I to V: all-atom root-mean-square differences for the 25S rRNA of the P stalk (nt 1223–1286) are within 2.5 Å. However, with respect to its position in the 80S•IRES complex in the absence of eEF2 and in the 80S•2tRNA•mRNA complex, the P stalk is shifted by ~13 Å toward the A site (Figure 2d).	RESULTS
4	21	sarcin-ricin loop	structure_element	The sarcin-ricin loop interacts with the GTP-binding site of eEF2 (Figures 5d and f).	RESULTS
41	57	GTP-binding site	site	The sarcin-ricin loop interacts with the GTP-binding site of eEF2 (Figures 5d and f).	RESULTS
61	65	eEF2	protein	The sarcin-ricin loop interacts with the GTP-binding site of eEF2 (Figures 5d and f).	RESULTS
70	78	70S•EF-G	complex_assembly	While the overall mode of this interaction is similar to that seen in 70S•EF-G crystal structures, there is an important local difference between Structure I and Structures II-V in switch loop I, as discussed below.	RESULTS
79	97	crystal structures	evidence	While the overall mode of this interaction is similar to that seen in 70S•EF-G crystal structures, there is an important local difference between Structure I and Structures II-V in switch loop I, as discussed below.	RESULTS
146	157	Structure I	evidence	While the overall mode of this interaction is similar to that seen in 70S•EF-G crystal structures, there is an important local difference between Structure I and Structures II-V in switch loop I, as discussed below.	RESULTS
162	177	Structures II-V	evidence	While the overall mode of this interaction is similar to that seen in 70S•EF-G crystal structures, there is an important local difference between Structure I and Structures II-V in switch loop I, as discussed below.	RESULTS
181	194	switch loop I	structure_element	While the overall mode of this interaction is similar to that seen in 70S•EF-G crystal structures, there is an important local difference between Structure I and Structures II-V in switch loop I, as discussed below.	RESULTS
31	57	positively-charged cluster	site	Repositioning (sliding) of the positively-charged cluster of domain IV of eEF2 over the phosphate backbone (red) of the 18S helices 33 and 34.	FIG
68	70	IV	structure_element	Repositioning (sliding) of the positively-charged cluster of domain IV of eEF2 over the phosphate backbone (red) of the 18S helices 33 and 34.	FIG
74	78	eEF2	protein	Repositioning (sliding) of the positively-charged cluster of domain IV of eEF2 over the phosphate backbone (red) of the 18S helices 33 and 34.	FIG
120	141	18S helices 33 and 34	structure_element	Repositioning (sliding) of the positively-charged cluster of domain IV of eEF2 over the phosphate backbone (red) of the 18S helices 33 and 34.	FIG
0	22	Structures I through V	evidence	Structures I through V are shown.	FIG
25	29	eEF2	protein	Electrostatic surface of eEF2 is shown; negatively and positively charged regions are shown in red and blue, respectively.	FIG
25	45	structural alignment	experimental_method	The view was obtained by structural alignment of the 18S rRNAs.	FIG
53	62	18S rRNAs	chemical	The view was obtained by structural alignment of the 18S rRNAs.	FIG
16	20	eEF2	protein	Interactions of eEF2 with the 40S subunit.	FIG
30	33	40S	complex_assembly	Interactions of eEF2 with the 40S subunit.	FIG
34	41	subunit	structure_element	Interactions of eEF2 with the 40S subunit.	FIG
4	8	eEF2	protein	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
41	45	body	structure_element	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
49	60	Structure I	evidence	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
62	66	eEF2	protein	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
136	140	head	structure_element	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
145	149	body	structure_element	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
153	176	Structures II through V	evidence	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
220	223	40S	complex_assembly	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
257	261	eEF2	protein	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
315	319	eEF2	protein	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
329	332	40S	complex_assembly	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
333	339	A site	site	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
346	367	Structure I through V	evidence	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
386	392	A-site	site	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
406	410	eEF2	protein	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
412	423	Structure V	evidence	(a) eEF2 (green) interacts only with the body in Structure I (eEF2 domains are labeled with roman numerals in white), and with both the head and body in Structures II through V. Colors are as in Figure 1, except for the 40S structural elements that contact eEF2, which are labeled and shown in purple. (b) Entry of eEF2 into the 40S A site, from Structure I through V. Distances to the A-site accommodated eEF2 (Structure V) are shown.	FIG
25	39	superpositions	experimental_method	The view was obtained by superpositions of the body domains of 18S rRNAs.	FIG
47	51	body	structure_element	The view was obtained by superpositions of the body domains of 18S rRNAs.	FIG
63	72	18S rRNAs	chemical	The view was obtained by superpositions of the body domains of 18S rRNAs.	FIG
25	46	Structure I through V	evidence	(c) Rearrangements, from Structure I through V, of a positively charged cluster of eEF2 (K613, R617 and R631) positioned over the phosphate backbone of 18S helices 33 and 34, suggesting a role of electrostatic interactions in eEF2 diffusion over the 40S surface.	FIG
83	87	eEF2	protein	(c) Rearrangements, from Structure I through V, of a positively charged cluster of eEF2 (K613, R617 and R631) positioned over the phosphate backbone of 18S helices 33 and 34, suggesting a role of electrostatic interactions in eEF2 diffusion over the 40S surface.	FIG
89	93	K613	residue_name_number	(c) Rearrangements, from Structure I through V, of a positively charged cluster of eEF2 (K613, R617 and R631) positioned over the phosphate backbone of 18S helices 33 and 34, suggesting a role of electrostatic interactions in eEF2 diffusion over the 40S surface.	FIG
95	99	R617	residue_name_number	(c) Rearrangements, from Structure I through V, of a positively charged cluster of eEF2 (K613, R617 and R631) positioned over the phosphate backbone of 18S helices 33 and 34, suggesting a role of electrostatic interactions in eEF2 diffusion over the 40S surface.	FIG
104	108	R631	residue_name_number	(c) Rearrangements, from Structure I through V, of a positively charged cluster of eEF2 (K613, R617 and R631) positioned over the phosphate backbone of 18S helices 33 and 34, suggesting a role of electrostatic interactions in eEF2 diffusion over the 40S surface.	FIG
152	173	18S helices 33 and 34	structure_element	(c) Rearrangements, from Structure I through V, of a positively charged cluster of eEF2 (K613, R617 and R631) positioned over the phosphate backbone of 18S helices 33 and 34, suggesting a role of electrostatic interactions in eEF2 diffusion over the 40S surface.	FIG
196	222	electrostatic interactions	bond_interaction	(c) Rearrangements, from Structure I through V, of a positively charged cluster of eEF2 (K613, R617 and R631) positioned over the phosphate backbone of 18S helices 33 and 34, suggesting a role of electrostatic interactions in eEF2 diffusion over the 40S surface.	FIG
226	230	eEF2	protein	(c) Rearrangements, from Structure I through V, of a positively charged cluster of eEF2 (K613, R617 and R631) positioned over the phosphate backbone of 18S helices 33 and 34, suggesting a role of electrostatic interactions in eEF2 diffusion over the 40S surface.	FIG
250	253	40S	complex_assembly	(c) Rearrangements, from Structure I through V, of a positively charged cluster of eEF2 (K613, R617 and R631) positioned over the phosphate backbone of 18S helices 33 and 34, suggesting a role of electrostatic interactions in eEF2 diffusion over the 40S surface.	FIG
31	34	III	structure_element	(d) Shift of the tip of domain III of eEF2, interacting with uS12 upon reverse subunit rotation from Structure I to Structure V. Structure I colored as in Figure 1, except uS12, which is in purple; Structure V is in gray.	FIG
38	42	eEF2	protein	(d) Shift of the tip of domain III of eEF2, interacting with uS12 upon reverse subunit rotation from Structure I to Structure V. Structure I colored as in Figure 1, except uS12, which is in purple; Structure V is in gray.	FIG
61	65	uS12	protein	(d) Shift of the tip of domain III of eEF2, interacting with uS12 upon reverse subunit rotation from Structure I to Structure V. Structure I colored as in Figure 1, except uS12, which is in purple; Structure V is in gray.	FIG
79	86	subunit	structure_element	(d) Shift of the tip of domain III of eEF2, interacting with uS12 upon reverse subunit rotation from Structure I to Structure V. Structure I colored as in Figure 1, except uS12, which is in purple; Structure V is in gray.	FIG
101	127	Structure I to Structure V	evidence	(d) Shift of the tip of domain III of eEF2, interacting with uS12 upon reverse subunit rotation from Structure I to Structure V. Structure I colored as in Figure 1, except uS12, which is in purple; Structure V is in gray.	FIG
129	140	Structure I	evidence	(d) Shift of the tip of domain III of eEF2, interacting with uS12 upon reverse subunit rotation from Structure I to Structure V. Structure I colored as in Figure 1, except uS12, which is in purple; Structure V is in gray.	FIG
172	176	uS12	protein	(d) Shift of the tip of domain III of eEF2, interacting with uS12 upon reverse subunit rotation from Structure I to Structure V. Structure I colored as in Figure 1, except uS12, which is in purple; Structure V is in gray.	FIG
198	209	Structure V	evidence	(d) Shift of the tip of domain III of eEF2, interacting with uS12 upon reverse subunit rotation from Structure I to Structure V. Structure I colored as in Figure 1, except uS12, which is in purple; Structure V is in gray.	FIG
66	84	Structures I and V	evidence	There are two modest but noticeable domain rearrangements between Structures I and V. Unlike in free eEF2, which can sample large movements of at least 50 Å of the C-terminal superdomain relative to the N-terminal superdomain (Figure 5c), eEF2 undergoes moderate repositioning of domain IV (~3 Å; Figure 5a) and domain III (~5 Å; Figure 6d).	RESULTS
96	100	free	protein_state	There are two modest but noticeable domain rearrangements between Structures I and V. Unlike in free eEF2, which can sample large movements of at least 50 Å of the C-terminal superdomain relative to the N-terminal superdomain (Figure 5c), eEF2 undergoes moderate repositioning of domain IV (~3 Å; Figure 5a) and domain III (~5 Å; Figure 6d).	RESULTS
101	105	eEF2	protein	There are two modest but noticeable domain rearrangements between Structures I and V. Unlike in free eEF2, which can sample large movements of at least 50 Å of the C-terminal superdomain relative to the N-terminal superdomain (Figure 5c), eEF2 undergoes moderate repositioning of domain IV (~3 Å; Figure 5a) and domain III (~5 Å; Figure 6d).	RESULTS
175	186	superdomain	structure_element	There are two modest but noticeable domain rearrangements between Structures I and V. Unlike in free eEF2, which can sample large movements of at least 50 Å of the C-terminal superdomain relative to the N-terminal superdomain (Figure 5c), eEF2 undergoes moderate repositioning of domain IV (~3 Å; Figure 5a) and domain III (~5 Å; Figure 6d).	RESULTS
214	225	superdomain	structure_element	There are two modest but noticeable domain rearrangements between Structures I and V. Unlike in free eEF2, which can sample large movements of at least 50 Å of the C-terminal superdomain relative to the N-terminal superdomain (Figure 5c), eEF2 undergoes moderate repositioning of domain IV (~3 Å; Figure 5a) and domain III (~5 Å; Figure 6d).	RESULTS
239	243	eEF2	protein	There are two modest but noticeable domain rearrangements between Structures I and V. Unlike in free eEF2, which can sample large movements of at least 50 Å of the C-terminal superdomain relative to the N-terminal superdomain (Figure 5c), eEF2 undergoes moderate repositioning of domain IV (~3 Å; Figure 5a) and domain III (~5 Å; Figure 6d).	RESULTS
287	289	IV	structure_element	There are two modest but noticeable domain rearrangements between Structures I and V. Unlike in free eEF2, which can sample large movements of at least 50 Å of the C-terminal superdomain relative to the N-terminal superdomain (Figure 5c), eEF2 undergoes moderate repositioning of domain IV (~3 Å; Figure 5a) and domain III (~5 Å; Figure 6d).	RESULTS
319	322	III	structure_element	There are two modest but noticeable domain rearrangements between Structures I and V. Unlike in free eEF2, which can sample large movements of at least 50 Å of the C-terminal superdomain relative to the N-terminal superdomain (Figure 5c), eEF2 undergoes moderate repositioning of domain IV (~3 Å; Figure 5a) and domain III (~5 Å; Figure 6d).	RESULTS
32	46	ribosome-bound	protein_state	This limited flexibility of the ribosome-bound eEF2 is likely the result of simultaneous fixation of eEF2 superdomains, via domains I and V, by the GTPase-associated center of the large subunit.	RESULTS
47	51	eEF2	protein	This limited flexibility of the ribosome-bound eEF2 is likely the result of simultaneous fixation of eEF2 superdomains, via domains I and V, by the GTPase-associated center of the large subunit.	RESULTS
101	105	eEF2	protein	This limited flexibility of the ribosome-bound eEF2 is likely the result of simultaneous fixation of eEF2 superdomains, via domains I and V, by the GTPase-associated center of the large subunit.	RESULTS
106	118	superdomains	structure_element	This limited flexibility of the ribosome-bound eEF2 is likely the result of simultaneous fixation of eEF2 superdomains, via domains I and V, by the GTPase-associated center of the large subunit.	RESULTS
132	133	I	structure_element	This limited flexibility of the ribosome-bound eEF2 is likely the result of simultaneous fixation of eEF2 superdomains, via domains I and V, by the GTPase-associated center of the large subunit.	RESULTS
138	139	V	structure_element	This limited flexibility of the ribosome-bound eEF2 is likely the result of simultaneous fixation of eEF2 superdomains, via domains I and V, by the GTPase-associated center of the large subunit.	RESULTS
148	172	GTPase-associated center	site	This limited flexibility of the ribosome-bound eEF2 is likely the result of simultaneous fixation of eEF2 superdomains, via domains I and V, by the GTPase-associated center of the large subunit.	RESULTS
180	193	large subunit	structure_element	This limited flexibility of the ribosome-bound eEF2 is likely the result of simultaneous fixation of eEF2 superdomains, via domains I and V, by the GTPase-associated center of the large subunit.	RESULTS
7	9	IV	structure_element	Domain IV of eEF2 binds at the 40S A site in Structures I to V but the mode of interaction differs in each complex (Figure 6).	RESULTS
13	17	eEF2	protein	Domain IV of eEF2 binds at the 40S A site in Structures I to V but the mode of interaction differs in each complex (Figure 6).	RESULTS
31	34	40S	complex_assembly	Domain IV of eEF2 binds at the 40S A site in Structures I to V but the mode of interaction differs in each complex (Figure 6).	RESULTS
35	41	A site	site	Domain IV of eEF2 binds at the 40S A site in Structures I to V but the mode of interaction differs in each complex (Figure 6).	RESULTS
45	62	Structures I to V	evidence	Domain IV of eEF2 binds at the 40S A site in Structures I to V but the mode of interaction differs in each complex (Figure 6).	RESULTS
8	12	eEF2	protein	Because eEF2 is rigidly attached to the 60S subunit and does not undergo large inter-subunit rearrangements, gradual entry of domain IV into the A site between Structures I and V is due to 40S subunit rotation and head swivel.	RESULTS
40	43	60S	complex_assembly	Because eEF2 is rigidly attached to the 60S subunit and does not undergo large inter-subunit rearrangements, gradual entry of domain IV into the A site between Structures I and V is due to 40S subunit rotation and head swivel.	RESULTS
44	51	subunit	structure_element	Because eEF2 is rigidly attached to the 60S subunit and does not undergo large inter-subunit rearrangements, gradual entry of domain IV into the A site between Structures I and V is due to 40S subunit rotation and head swivel.	RESULTS
85	92	subunit	structure_element	Because eEF2 is rigidly attached to the 60S subunit and does not undergo large inter-subunit rearrangements, gradual entry of domain IV into the A site between Structures I and V is due to 40S subunit rotation and head swivel.	RESULTS
133	135	IV	structure_element	Because eEF2 is rigidly attached to the 60S subunit and does not undergo large inter-subunit rearrangements, gradual entry of domain IV into the A site between Structures I and V is due to 40S subunit rotation and head swivel.	RESULTS
145	151	A site	site	Because eEF2 is rigidly attached to the 60S subunit and does not undergo large inter-subunit rearrangements, gradual entry of domain IV into the A site between Structures I and V is due to 40S subunit rotation and head swivel.	RESULTS
160	178	Structures I and V	evidence	Because eEF2 is rigidly attached to the 60S subunit and does not undergo large inter-subunit rearrangements, gradual entry of domain IV into the A site between Structures I and V is due to 40S subunit rotation and head swivel.	RESULTS
189	192	40S	complex_assembly	Because eEF2 is rigidly attached to the 60S subunit and does not undergo large inter-subunit rearrangements, gradual entry of domain IV into the A site between Structures I and V is due to 40S subunit rotation and head swivel.	RESULTS
193	200	subunit	structure_element	Because eEF2 is rigidly attached to the 60S subunit and does not undergo large inter-subunit rearrangements, gradual entry of domain IV into the A site between Structures I and V is due to 40S subunit rotation and head swivel.	RESULTS
214	218	head	structure_element	Because eEF2 is rigidly attached to the 60S subunit and does not undergo large inter-subunit rearrangements, gradual entry of domain IV into the A site between Structures I and V is due to 40S subunit rotation and head swivel.	RESULTS
0	4	eEF2	protein	eEF2 settles into the A site from Structure I to V, as the tip of domain IV shifts by ~10 Å relative to the body and by ~20 Å relative to the swiveling head.	RESULTS
22	28	A site	site	eEF2 settles into the A site from Structure I to V, as the tip of domain IV shifts by ~10 Å relative to the body and by ~20 Å relative to the swiveling head.	RESULTS
34	50	Structure I to V	evidence	eEF2 settles into the A site from Structure I to V, as the tip of domain IV shifts by ~10 Å relative to the body and by ~20 Å relative to the swiveling head.	RESULTS
73	75	IV	structure_element	eEF2 settles into the A site from Structure I to V, as the tip of domain IV shifts by ~10 Å relative to the body and by ~20 Å relative to the swiveling head.	RESULTS
108	112	body	structure_element	eEF2 settles into the A site from Structure I to V, as the tip of domain IV shifts by ~10 Å relative to the body and by ~20 Å relative to the swiveling head.	RESULTS
152	156	head	structure_element	eEF2 settles into the A site from Structure I to V, as the tip of domain IV shifts by ~10 Å relative to the body and by ~20 Å relative to the swiveling head.	RESULTS
13	17	eEF2	protein	Modest intra-eEF2 shifts of domain IV between Structures I to V outline a stochastic trajectory (Figure 5a), consistent with local adjustments of the domain in the A site.	RESULTS
35	37	IV	structure_element	Modest intra-eEF2 shifts of domain IV between Structures I to V outline a stochastic trajectory (Figure 5a), consistent with local adjustments of the domain in the A site.	RESULTS
46	63	Structures I to V	evidence	Modest intra-eEF2 shifts of domain IV between Structures I to V outline a stochastic trajectory (Figure 5a), consistent with local adjustments of the domain in the A site.	RESULTS
164	170	A site	site	Modest intra-eEF2 shifts of domain IV between Structures I to V outline a stochastic trajectory (Figure 5a), consistent with local adjustments of the domain in the A site.	RESULTS
25	29	eEF2	protein	At the central region of eEF2, domains II and III contact the 40S body (mainly at nucleotides 48–52 and 429–432 of 18S rRNA helix 5 and uS12).	RESULTS
39	41	II	structure_element	At the central region of eEF2, domains II and III contact the 40S body (mainly at nucleotides 48–52 and 429–432 of 18S rRNA helix 5 and uS12).	RESULTS
46	49	III	structure_element	At the central region of eEF2, domains II and III contact the 40S body (mainly at nucleotides 48–52 and 429–432 of 18S rRNA helix 5 and uS12).	RESULTS
62	65	40S	complex_assembly	At the central region of eEF2, domains II and III contact the 40S body (mainly at nucleotides 48–52 and 429–432 of 18S rRNA helix 5 and uS12).	RESULTS
66	70	body	structure_element	At the central region of eEF2, domains II and III contact the 40S body (mainly at nucleotides 48–52 and 429–432 of 18S rRNA helix 5 and uS12).	RESULTS
94	99	48–52	residue_range	At the central region of eEF2, domains II and III contact the 40S body (mainly at nucleotides 48–52 and 429–432 of 18S rRNA helix 5 and uS12).	RESULTS
104	111	429–432	residue_range	At the central region of eEF2, domains II and III contact the 40S body (mainly at nucleotides 48–52 and 429–432 of 18S rRNA helix 5 and uS12).	RESULTS
115	123	18S rRNA	chemical	At the central region of eEF2, domains II and III contact the 40S body (mainly at nucleotides 48–52 and 429–432 of 18S rRNA helix 5 and uS12).	RESULTS
124	131	helix 5	structure_element	At the central region of eEF2, domains II and III contact the 40S body (mainly at nucleotides 48–52 and 429–432 of 18S rRNA helix 5 and uS12).	RESULTS
136	140	uS12	protein	At the central region of eEF2, domains II and III contact the 40S body (mainly at nucleotides 48–52 and 429–432 of 18S rRNA helix 5 and uS12).	RESULTS
5	21	Structure I to V	evidence	From Structure I to V, these central domains migrate by ~10 Å along the 40S surface (Figure 6c).	RESULTS
72	75	40S	complex_assembly	From Structure I to V, these central domains migrate by ~10 Å along the 40S surface (Figure 6c).	RESULTS
14	18	eEF2	protein	Comparison of eEF2 conformations reveals that in Structure V, domain III is displaced as a result of interaction with uS12, as discussed below.	RESULTS
49	60	Structure V	evidence	Comparison of eEF2 conformations reveals that in Structure V, domain III is displaced as a result of interaction with uS12, as discussed below.	RESULTS
69	72	III	structure_element	Comparison of eEF2 conformations reveals that in Structure V, domain III is displaced as a result of interaction with uS12, as discussed below.	RESULTS
118	122	uS12	protein	Comparison of eEF2 conformations reveals that in Structure V, domain III is displaced as a result of interaction with uS12, as discussed below.	RESULTS
20	38	Structures I and V	evidence	In summary, between Structures I and V, a step-wise translocation of PKI by ~15 Å from the A to P site - within the 40S subunit – occurs simultaneously with the ~11 Å side-way entry of domain IV into the A site coupled with ~3 to 5 Å inter-domain rearrangements in eEF2.	RESULTS
69	72	PKI	structure_element	In summary, between Structures I and V, a step-wise translocation of PKI by ~15 Å from the A to P site - within the 40S subunit – occurs simultaneously with the ~11 Å side-way entry of domain IV into the A site coupled with ~3 to 5 Å inter-domain rearrangements in eEF2.	RESULTS
91	102	A to P site	site	In summary, between Structures I and V, a step-wise translocation of PKI by ~15 Å from the A to P site - within the 40S subunit – occurs simultaneously with the ~11 Å side-way entry of domain IV into the A site coupled with ~3 to 5 Å inter-domain rearrangements in eEF2.	RESULTS
116	119	40S	complex_assembly	In summary, between Structures I and V, a step-wise translocation of PKI by ~15 Å from the A to P site - within the 40S subunit – occurs simultaneously with the ~11 Å side-way entry of domain IV into the A site coupled with ~3 to 5 Å inter-domain rearrangements in eEF2.	RESULTS
120	127	subunit	structure_element	In summary, between Structures I and V, a step-wise translocation of PKI by ~15 Å from the A to P site - within the 40S subunit – occurs simultaneously with the ~11 Å side-way entry of domain IV into the A site coupled with ~3 to 5 Å inter-domain rearrangements in eEF2.	RESULTS
192	194	IV	structure_element	In summary, between Structures I and V, a step-wise translocation of PKI by ~15 Å from the A to P site - within the 40S subunit – occurs simultaneously with the ~11 Å side-way entry of domain IV into the A site coupled with ~3 to 5 Å inter-domain rearrangements in eEF2.	RESULTS
204	210	A site	site	In summary, between Structures I and V, a step-wise translocation of PKI by ~15 Å from the A to P site - within the 40S subunit – occurs simultaneously with the ~11 Å side-way entry of domain IV into the A site coupled with ~3 to 5 Å inter-domain rearrangements in eEF2.	RESULTS
265	269	eEF2	protein	In summary, between Structures I and V, a step-wise translocation of PKI by ~15 Å from the A to P site - within the 40S subunit – occurs simultaneously with the ~11 Å side-way entry of domain IV into the A site coupled with ~3 to 5 Å inter-domain rearrangements in eEF2.	RESULTS
54	57	40S	complex_assembly	These shifts occur during the reverse rotation of the 40S body coupled with the forward-then-reverse head swivel.	RESULTS
58	62	body	structure_element	These shifts occur during the reverse rotation of the 40S body coupled with the forward-then-reverse head swivel.	RESULTS
101	105	head	structure_element	These shifts occur during the reverse rotation of the 40S body coupled with the forward-then-reverse head swivel.	RESULTS
50	54	IRES	site	To elucidate the detailed structural mechanism of IRES translocation and the roles of eEF2 and ribosome rearrangements, we describe in the following sections the interactions of PKI and eEF2 with the ribosomal A and P sites in Structures I through V (Figure 2g; see also Figure 1—figure supplement 1).	RESULTS
86	90	eEF2	protein	To elucidate the detailed structural mechanism of IRES translocation and the roles of eEF2 and ribosome rearrangements, we describe in the following sections the interactions of PKI and eEF2 with the ribosomal A and P sites in Structures I through V (Figure 2g; see also Figure 1—figure supplement 1).	RESULTS
95	103	ribosome	complex_assembly	To elucidate the detailed structural mechanism of IRES translocation and the roles of eEF2 and ribosome rearrangements, we describe in the following sections the interactions of PKI and eEF2 with the ribosomal A and P sites in Structures I through V (Figure 2g; see also Figure 1—figure supplement 1).	RESULTS
178	181	PKI	structure_element	To elucidate the detailed structural mechanism of IRES translocation and the roles of eEF2 and ribosome rearrangements, we describe in the following sections the interactions of PKI and eEF2 with the ribosomal A and P sites in Structures I through V (Figure 2g; see also Figure 1—figure supplement 1).	RESULTS
186	190	eEF2	protein	To elucidate the detailed structural mechanism of IRES translocation and the roles of eEF2 and ribosome rearrangements, we describe in the following sections the interactions of PKI and eEF2 with the ribosomal A and P sites in Structures I through V (Figure 2g; see also Figure 1—figure supplement 1).	RESULTS
210	223	A and P sites	site	To elucidate the detailed structural mechanism of IRES translocation and the roles of eEF2 and ribosome rearrangements, we describe in the following sections the interactions of PKI and eEF2 with the ribosomal A and P sites in Structures I through V (Figure 2g; see also Figure 1—figure supplement 1).	RESULTS
227	249	Structures I through V	evidence	To elucidate the detailed structural mechanism of IRES translocation and the roles of eEF2 and ribosome rearrangements, we describe in the following sections the interactions of PKI and eEF2 with the ribosomal A and P sites in Structures I through V (Figure 2g; see also Figure 1—figure supplement 1).	RESULTS
0	11	Structure I	evidence	Structure I represents a pre-translocation IRES and initial entry of eEF2 in a GTP-like state	RESULTS
25	42	pre-translocation	protein_state	Structure I represents a pre-translocation IRES and initial entry of eEF2 in a GTP-like state	RESULTS
43	47	IRES	site	Structure I represents a pre-translocation IRES and initial entry of eEF2 in a GTP-like state	RESULTS
69	73	eEF2	protein	Structure I represents a pre-translocation IRES and initial entry of eEF2 in a GTP-like state	RESULTS
79	82	GTP	chemical	Structure I represents a pre-translocation IRES and initial entry of eEF2 in a GTP-like state	RESULTS
7	20	fully rotated	protein_state	In the fully rotated Structure I, PKI is shifted toward the P site by ~3 Å relative to its position in the initiation complex but maintains interactions with the partially swiveled head.	RESULTS
21	32	Structure I	evidence	In the fully rotated Structure I, PKI is shifted toward the P site by ~3 Å relative to its position in the initiation complex but maintains interactions with the partially swiveled head.	RESULTS
34	37	PKI	structure_element	In the fully rotated Structure I, PKI is shifted toward the P site by ~3 Å relative to its position in the initiation complex but maintains interactions with the partially swiveled head.	RESULTS
60	66	P site	site	In the fully rotated Structure I, PKI is shifted toward the P site by ~3 Å relative to its position in the initiation complex but maintains interactions with the partially swiveled head.	RESULTS
107	125	initiation complex	complex_assembly	In the fully rotated Structure I, PKI is shifted toward the P site by ~3 Å relative to its position in the initiation complex but maintains interactions with the partially swiveled head.	RESULTS
162	180	partially swiveled	protein_state	In the fully rotated Structure I, PKI is shifted toward the P site by ~3 Å relative to its position in the initiation complex but maintains interactions with the partially swiveled head.	RESULTS
181	185	head	structure_element	In the fully rotated Structure I, PKI is shifted toward the P site by ~3 Å relative to its position in the initiation complex but maintains interactions with the partially swiveled head.	RESULTS
7	11	head	structure_element	At the head, C1274 of the 18S rRNA (C1054 in E. coli) base pairs with the first nucleotide of the ORF immediately downstream of PKI.	RESULTS
13	18	C1274	residue_name_number	At the head, C1274 of the 18S rRNA (C1054 in E. coli) base pairs with the first nucleotide of the ORF immediately downstream of PKI.	RESULTS
26	34	18S rRNA	chemical	At the head, C1274 of the 18S rRNA (C1054 in E. coli) base pairs with the first nucleotide of the ORF immediately downstream of PKI.	RESULTS
36	41	C1054	residue_name_number	At the head, C1274 of the 18S rRNA (C1054 in E. coli) base pairs with the first nucleotide of the ORF immediately downstream of PKI.	RESULTS
45	52	E. coli	species	At the head, C1274 of the 18S rRNA (C1054 in E. coli) base pairs with the first nucleotide of the ORF immediately downstream of PKI.	RESULTS
98	101	ORF	structure_element	At the head, C1274 of the 18S rRNA (C1054 in E. coli) base pairs with the first nucleotide of the ORF immediately downstream of PKI.	RESULTS
128	131	PKI	structure_element	At the head, C1274 of the 18S rRNA (C1054 in E. coli) base pairs with the first nucleotide of the ORF immediately downstream of PKI.	RESULTS
4	9	C1274	residue_name_number	The C1274:G6953 base pair provides a stacking platform for the codon-anticodon–like helix of PKI.	RESULTS
10	15	G6953	residue_name_number	The C1274:G6953 base pair provides a stacking platform for the codon-anticodon–like helix of PKI.	RESULTS
37	54	stacking platform	site	The C1274:G6953 base pair provides a stacking platform for the codon-anticodon–like helix of PKI.	RESULTS
63	89	codon-anticodon–like helix	structure_element	The C1274:G6953 base pair provides a stacking platform for the codon-anticodon–like helix of PKI.	RESULTS
93	96	PKI	structure_element	The C1274:G6953 base pair provides a stacking platform for the codon-anticodon–like helix of PKI.	RESULTS
20	25	C1274	residue_name_number	We therefore define C1274 as the foundation of the 'head A site'.	RESULTS
52	56	head	structure_element	We therefore define C1274 as the foundation of the 'head A site'.	RESULTS
57	63	A site	site	We therefore define C1274 as the foundation of the 'head A site'.	RESULTS
20	25	U1191	residue_name_number	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
27	31	G966	residue_name_number	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
35	42	E. coli	species	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
48	53	C1637	residue_name_number	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
55	60	C1400	residue_name_number	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
64	71	E. coli	species	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
105	109	head	structure_element	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
110	116	P site	site	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
123	127	body	structure_element	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
128	134	P site	site	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
224	242	fully translocated	protein_state	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
243	258	mRNA-tRNA helix	structure_element	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
262	272	tRNA-bound	protein_state	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
273	283	structures	evidence	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
295	313	post-translocation	protein_state	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
314	325	Structure V	evidence	Accordingly, we use U1191 (G966 in E. coli) and C1637 (C1400 in E. coli) as the reference points of the 'head P site' and 'body P site' (Figure 2g), respectively, because these nucleotides form a stacking foundation for the fully translocated mRNA-tRNA helix in tRNA-bound structures and in our post-translocation Structure V discussed below.	RESULTS
36	40	eEF2	protein	Interactions of the residues at the eEF2 tip with the decoding center of the IRES-bound ribosome.	FIG
54	69	decoding center	site	Interactions of the residues at the eEF2 tip with the decoding center of the IRES-bound ribosome.	FIG
77	87	IRES-bound	protein_state	Interactions of the residues at the eEF2 tip with the decoding center of the IRES-bound ribosome.	FIG
88	96	ribosome	complex_assembly	Interactions of the residues at the eEF2 tip with the decoding center of the IRES-bound ribosome.	FIG
20	35	decoding center	site	Key elements of the decoding center of the 'locked' initiation structure, 'unlocked' Structure I, and post-translocation Structure V (this work) are shown.	FIG
44	50	locked	protein_state	Key elements of the decoding center of the 'locked' initiation structure, 'unlocked' Structure I, and post-translocation Structure V (this work) are shown.	FIG
52	62	initiation	protein_state	Key elements of the decoding center of the 'locked' initiation structure, 'unlocked' Structure I, and post-translocation Structure V (this work) are shown.	FIG
63	72	structure	evidence	Key elements of the decoding center of the 'locked' initiation structure, 'unlocked' Structure I, and post-translocation Structure V (this work) are shown.	FIG
75	83	unlocked	protein_state	Key elements of the decoding center of the 'locked' initiation structure, 'unlocked' Structure I, and post-translocation Structure V (this work) are shown.	FIG
85	96	Structure I	evidence	Key elements of the decoding center of the 'locked' initiation structure, 'unlocked' Structure I, and post-translocation Structure V (this work) are shown.	FIG
102	120	post-translocation	protein_state	Key elements of the decoding center of the 'locked' initiation structure, 'unlocked' Structure I, and post-translocation Structure V (this work) are shown.	FIG
121	132	Structure V	evidence	Key elements of the decoding center of the 'locked' initiation structure, 'unlocked' Structure I, and post-translocation Structure V (this work) are shown.	FIG
4	29	histidine-diphthamide tip	site	The histidine-diphthamide tip of eEF2 is shown in green.	FIG
33	37	eEF2	protein	The histidine-diphthamide tip of eEF2 is shown in green.	FIG
4	30	codon-anticodon-like helix	structure_element	The codon-anticodon-like helix of PKI is shown in red, the downstream first codon of the ORF in magenta.	FIG
34	37	PKI	structure_element	The codon-anticodon-like helix of PKI is shown in red, the downstream first codon of the ORF in magenta.	FIG
89	92	ORF	structure_element	The codon-anticodon-like helix of PKI is shown in red, the downstream first codon of the ORF in magenta.	FIG
19	27	18S rRNA	chemical	Nucleotides of the 18S rRNA body are in orange and head in yellow; 25S rRNA nucleotide A2256 is blue.	FIG
28	32	body	structure_element	Nucleotides of the 18S rRNA body are in orange and head in yellow; 25S rRNA nucleotide A2256 is blue.	FIG
51	55	head	structure_element	Nucleotides of the 18S rRNA body are in orange and head in yellow; 25S rRNA nucleotide A2256 is blue.	FIG
67	75	25S rRNA	chemical	Nucleotides of the 18S rRNA body are in orange and head in yellow; 25S rRNA nucleotide A2256 is blue.	FIG
87	92	A2256	residue_name_number	Nucleotides of the 18S rRNA body are in orange and head in yellow; 25S rRNA nucleotide A2256 is blue.	FIG
0	13	A and P sites	site	A and P sites are schematically demarcated by dotted lines.	FIG
19	22	PKI	structure_element	The interaction of PKI with the 40S body is substantially rearranged relative to that in the initiation state.	RESULTS
32	35	40S	complex_assembly	The interaction of PKI with the 40S body is substantially rearranged relative to that in the initiation state.	RESULTS
36	40	body	structure_element	The interaction of PKI with the 40S body is substantially rearranged relative to that in the initiation state.	RESULTS
93	103	initiation	protein_state	The interaction of PKI with the 40S body is substantially rearranged relative to that in the initiation state.	RESULTS
15	18	PKI	structure_element	In the latter, PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 ('body A site'), as in the A-site tRNA bound complexes.	RESULTS
58	79	universally conserved	protein_state	In the latter, PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 ('body A site'), as in the A-site tRNA bound complexes.	RESULTS
80	95	decoding-center	site	In the latter, PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 ('body A site'), as in the A-site tRNA bound complexes.	RESULTS
108	112	G577	residue_name_number	In the latter, PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 ('body A site'), as in the A-site tRNA bound complexes.	RESULTS
114	119	A1755	residue_name_number	In the latter, PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 ('body A site'), as in the A-site tRNA bound complexes.	RESULTS
124	129	A1756	residue_name_number	In the latter, PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 ('body A site'), as in the A-site tRNA bound complexes.	RESULTS
132	136	body	structure_element	In the latter, PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 ('body A site'), as in the A-site tRNA bound complexes.	RESULTS
137	143	A site	site	In the latter, PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 ('body A site'), as in the A-site tRNA bound complexes.	RESULTS
157	163	A-site	site	In the latter, PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 ('body A site'), as in the A-site tRNA bound complexes.	RESULTS
164	174	tRNA bound	protein_state	In the latter, PKI is stabilized by interactions with the universally conserved decoding-center nucleotides G577, A1755 and A1756 ('body A site'), as in the A-site tRNA bound complexes.	RESULTS
3	14	Structure I	evidence	In Structure I, PKI does not contact these nucleotides (Figures 2g and 7).	RESULTS
16	19	PKI	structure_element	In Structure I, PKI does not contact these nucleotides (Figures 2g and 7).	RESULTS
16	20	eEF2	protein	The position of eEF2 on the 40S subunit of Structure I is markedly distinct from those in Structures II to V. The translocase interacts with the 40S body but does not contact the head (Figures 5b and 6a; Figure 5—figure supplement 1).	RESULTS
28	31	40S	complex_assembly	The position of eEF2 on the 40S subunit of Structure I is markedly distinct from those in Structures II to V. The translocase interacts with the 40S body but does not contact the head (Figures 5b and 6a; Figure 5—figure supplement 1).	RESULTS
32	39	subunit	structure_element	The position of eEF2 on the 40S subunit of Structure I is markedly distinct from those in Structures II to V. The translocase interacts with the 40S body but does not contact the head (Figures 5b and 6a; Figure 5—figure supplement 1).	RESULTS
32	39	subunit	structure_element	The position of eEF2 on the 40S subunit of Structure I is markedly distinct from those in Structures II to V. The translocase interacts with the 40S body but does not contact the head (Figures 5b and 6a; Figure 5—figure supplement 1).	RESULTS
43	54	Structure I	evidence	The position of eEF2 on the 40S subunit of Structure I is markedly distinct from those in Structures II to V. The translocase interacts with the 40S body but does not contact the head (Figures 5b and 6a; Figure 5—figure supplement 1).	RESULTS
90	108	Structures II to V	evidence	The position of eEF2 on the 40S subunit of Structure I is markedly distinct from those in Structures II to V. The translocase interacts with the 40S body but does not contact the head (Figures 5b and 6a; Figure 5—figure supplement 1).	RESULTS
114	125	translocase	protein_type	The position of eEF2 on the 40S subunit of Structure I is markedly distinct from those in Structures II to V. The translocase interacts with the 40S body but does not contact the head (Figures 5b and 6a; Figure 5—figure supplement 1).	RESULTS
145	148	40S	complex_assembly	The position of eEF2 on the 40S subunit of Structure I is markedly distinct from those in Structures II to V. The translocase interacts with the 40S body but does not contact the head (Figures 5b and 6a; Figure 5—figure supplement 1).	RESULTS
149	153	body	structure_element	The position of eEF2 on the 40S subunit of Structure I is markedly distinct from those in Structures II to V. The translocase interacts with the 40S body but does not contact the head (Figures 5b and 6a; Figure 5—figure supplement 1).	RESULTS
179	183	head	structure_element	The position of eEF2 on the 40S subunit of Structure I is markedly distinct from those in Structures II to V. The translocase interacts with the 40S body but does not contact the head (Figures 5b and 6a; Figure 5—figure supplement 1).	RESULTS
7	9	IV	structure_element	Domain IV is partially engaged with the body A site.	RESULTS
40	44	body	structure_element	Domain IV is partially engaged with the body A site.	RESULTS
45	51	A site	site	Domain IV is partially engaged with the body A site.	RESULTS
18	20	IV	structure_element	The tip of domain IV is wedged between PKI and decoding-center nucleotides A1755 and A1756, which are bulged out of h44.	RESULTS
39	42	PKI	structure_element	The tip of domain IV is wedged between PKI and decoding-center nucleotides A1755 and A1756, which are bulged out of h44.	RESULTS
47	62	decoding-center	site	The tip of domain IV is wedged between PKI and decoding-center nucleotides A1755 and A1756, which are bulged out of h44.	RESULTS
75	80	A1755	residue_name_number	The tip of domain IV is wedged between PKI and decoding-center nucleotides A1755 and A1756, which are bulged out of h44.	RESULTS
85	90	A1756	residue_name_number	The tip of domain IV is wedged between PKI and decoding-center nucleotides A1755 and A1756, which are bulged out of h44.	RESULTS
22	49	histidine-diphthamide triad	site	This tip contains the histidine-diphthamide triad (H583, H694 and Diph699), which interacts with the codon-anticodon-like helix of PKI and A1756 (Figure 7).	RESULTS
51	55	H583	residue_name_number	This tip contains the histidine-diphthamide triad (H583, H694 and Diph699), which interacts with the codon-anticodon-like helix of PKI and A1756 (Figure 7).	RESULTS
57	61	H694	residue_name_number	This tip contains the histidine-diphthamide triad (H583, H694 and Diph699), which interacts with the codon-anticodon-like helix of PKI and A1756 (Figure 7).	RESULTS
66	73	Diph699	ptm	This tip contains the histidine-diphthamide triad (H583, H694 and Diph699), which interacts with the codon-anticodon-like helix of PKI and A1756 (Figure 7).	RESULTS
101	127	codon-anticodon-like helix	structure_element	This tip contains the histidine-diphthamide triad (H583, H694 and Diph699), which interacts with the codon-anticodon-like helix of PKI and A1756 (Figure 7).	RESULTS
131	134	PKI	structure_element	This tip contains the histidine-diphthamide triad (H583, H694 and Diph699), which interacts with the codon-anticodon-like helix of PKI and A1756 (Figure 7).	RESULTS
139	144	A1756	residue_name_number	This tip contains the histidine-diphthamide triad (H583, H694 and Diph699), which interacts with the codon-anticodon-like helix of PKI and A1756 (Figure 7).	RESULTS
0	22	Histidines 583 and 694	residue_name_number	Histidines 583 and 694 interact with the phosphate backbone of the anticodon-like strand (at G6907 and C6908).	RESULTS
67	88	anticodon-like strand	structure_element	Histidines 583 and 694 interact with the phosphate backbone of the anticodon-like strand (at G6907 and C6908).	RESULTS
93	98	G6907	residue_name_number	Histidines 583 and 694 interact with the phosphate backbone of the anticodon-like strand (at G6907 and C6908).	RESULTS
103	108	C6908	residue_name_number	Histidines 583 and 694 interact with the phosphate backbone of the anticodon-like strand (at G6907 and C6908).	RESULTS
0	11	Diphthamide	ptm	Diphthamide is a unique posttranslational modification conserved in archaeal and eukaryotic EF2 (at residue 699 in S. cerevisiae) and involves addition of a ~7-Å long 3-carboxyamido-3-(trimethylamino)-propyl moiety to the histidine imidazole ring at CE1.	RESULTS
55	64	conserved	protein_state	Diphthamide is a unique posttranslational modification conserved in archaeal and eukaryotic EF2 (at residue 699 in S. cerevisiae) and involves addition of a ~7-Å long 3-carboxyamido-3-(trimethylamino)-propyl moiety to the histidine imidazole ring at CE1.	RESULTS
68	76	archaeal	taxonomy_domain	Diphthamide is a unique posttranslational modification conserved in archaeal and eukaryotic EF2 (at residue 699 in S. cerevisiae) and involves addition of a ~7-Å long 3-carboxyamido-3-(trimethylamino)-propyl moiety to the histidine imidazole ring at CE1.	RESULTS
81	91	eukaryotic	taxonomy_domain	Diphthamide is a unique posttranslational modification conserved in archaeal and eukaryotic EF2 (at residue 699 in S. cerevisiae) and involves addition of a ~7-Å long 3-carboxyamido-3-(trimethylamino)-propyl moiety to the histidine imidazole ring at CE1.	RESULTS
92	95	EF2	protein	Diphthamide is a unique posttranslational modification conserved in archaeal and eukaryotic EF2 (at residue 699 in S. cerevisiae) and involves addition of a ~7-Å long 3-carboxyamido-3-(trimethylamino)-propyl moiety to the histidine imidazole ring at CE1.	RESULTS
108	111	699	residue_number	Diphthamide is a unique posttranslational modification conserved in archaeal and eukaryotic EF2 (at residue 699 in S. cerevisiae) and involves addition of a ~7-Å long 3-carboxyamido-3-(trimethylamino)-propyl moiety to the histidine imidazole ring at CE1.	RESULTS
115	128	S. cerevisiae	species	Diphthamide is a unique posttranslational modification conserved in archaeal and eukaryotic EF2 (at residue 699 in S. cerevisiae) and involves addition of a ~7-Å long 3-carboxyamido-3-(trimethylamino)-propyl moiety to the histidine imidazole ring at CE1.	RESULTS
222	231	histidine	residue_name	Diphthamide is a unique posttranslational modification conserved in archaeal and eukaryotic EF2 (at residue 699 in S. cerevisiae) and involves addition of a ~7-Å long 3-carboxyamido-3-(trimethylamino)-propyl moiety to the histidine imidazole ring at CE1.	RESULTS
26	33	Diph699	ptm	The trimethylamino end of Diph699 packs over A1756 (Figure 7).	RESULTS
45	50	A1756	residue_name_number	The trimethylamino end of Diph699 packs over A1756 (Figure 7).	RESULTS
56	68	minor-groove	site	The opposite surface of the tail is oriented toward the minor-groove side of the second base pair of the codon-anticodon helix (G6906:C6951).	RESULTS
105	126	codon-anticodon helix	structure_element	The opposite surface of the tail is oriented toward the minor-groove side of the second base pair of the codon-anticodon helix (G6906:C6951).	RESULTS
128	133	G6906	residue_name_number	The opposite surface of the tail is oriented toward the minor-groove side of the second base pair of the codon-anticodon helix (G6906:C6951).	RESULTS
134	139	C6951	residue_name_number	The opposite surface of the tail is oriented toward the minor-groove side of the second base pair of the codon-anticodon helix (G6906:C6951).	RESULTS
29	39	initiation	protein_state	Thus, in comparison with the initiation state, the histidine-diphthamide tip of eEF2 replaces the codon-anticodon–like helix of PKI.	RESULTS
51	76	histidine-diphthamide tip	site	Thus, in comparison with the initiation state, the histidine-diphthamide tip of eEF2 replaces the codon-anticodon–like helix of PKI.	RESULTS
80	84	eEF2	protein	Thus, in comparison with the initiation state, the histidine-diphthamide tip of eEF2 replaces the codon-anticodon–like helix of PKI.	RESULTS
98	124	codon-anticodon–like helix	structure_element	Thus, in comparison with the initiation state, the histidine-diphthamide tip of eEF2 replaces the codon-anticodon–like helix of PKI.	RESULTS
128	131	PKI	structure_element	Thus, in comparison with the initiation state, the histidine-diphthamide tip of eEF2 replaces the codon-anticodon–like helix of PKI.	RESULTS
36	41	A1755	residue_name_number	The splitting of the interaction of A1755-A1756 and PKI is achieved by providing the histidine-diphthamine tip as a binding partner for both A1756 and the minor groove of the codon-anticodon helix (Figure 7).	RESULTS
42	47	A1756	residue_name_number	The splitting of the interaction of A1755-A1756 and PKI is achieved by providing the histidine-diphthamine tip as a binding partner for both A1756 and the minor groove of the codon-anticodon helix (Figure 7).	RESULTS
52	55	PKI	structure_element	The splitting of the interaction of A1755-A1756 and PKI is achieved by providing the histidine-diphthamine tip as a binding partner for both A1756 and the minor groove of the codon-anticodon helix (Figure 7).	RESULTS
85	110	histidine-diphthamine tip	site	The splitting of the interaction of A1755-A1756 and PKI is achieved by providing the histidine-diphthamine tip as a binding partner for both A1756 and the minor groove of the codon-anticodon helix (Figure 7).	RESULTS
141	146	A1756	residue_name_number	The splitting of the interaction of A1755-A1756 and PKI is achieved by providing the histidine-diphthamine tip as a binding partner for both A1756 and the minor groove of the codon-anticodon helix (Figure 7).	RESULTS
155	167	minor groove	site	The splitting of the interaction of A1755-A1756 and PKI is achieved by providing the histidine-diphthamine tip as a binding partner for both A1756 and the minor groove of the codon-anticodon helix (Figure 7).	RESULTS
175	196	codon-anticodon helix	structure_element	The splitting of the interaction of A1755-A1756 and PKI is achieved by providing the histidine-diphthamine tip as a binding partner for both A1756 and the minor groove of the codon-anticodon helix (Figure 7).	RESULTS
10	28	Structures II to V	evidence	Unlike in Structures II to V, the conformation of the eEF2 GTPase center in Structure I resembles that of a GTP-bound translocase (Figure 5e).	RESULTS
54	58	eEF2	protein	Unlike in Structures II to V, the conformation of the eEF2 GTPase center in Structure I resembles that of a GTP-bound translocase (Figure 5e).	RESULTS
59	72	GTPase center	site	Unlike in Structures II to V, the conformation of the eEF2 GTPase center in Structure I resembles that of a GTP-bound translocase (Figure 5e).	RESULTS
76	87	Structure I	evidence	Unlike in Structures II to V, the conformation of the eEF2 GTPase center in Structure I resembles that of a GTP-bound translocase (Figure 5e).	RESULTS
108	117	GTP-bound	protein_state	Unlike in Structures II to V, the conformation of the eEF2 GTPase center in Structure I resembles that of a GTP-bound translocase (Figure 5e).	RESULTS
118	129	translocase	protein_type	Unlike in Structures II to V, the conformation of the eEF2 GTPase center in Structure I resembles that of a GTP-bound translocase (Figure 5e).	RESULTS
3	24	translational GTPases	protein_type	In translational GTPases, switch loops I and II are involved in the GTPase activity (reviewed in).	RESULTS
26	47	switch loops I and II	structure_element	In translational GTPases, switch loops I and II are involved in the GTPase activity (reviewed in).	RESULTS
68	74	GTPase	protein_type	In translational GTPases, switch loops I and II are involved in the GTPase activity (reviewed in).	RESULTS
0	14	Switch loop II	structure_element	Switch loop II (aa 105–110), which carries the catalytic H108 (H92 in E. coli EF-G; is well resolved in all five structures.	RESULTS
19	26	105–110	residue_range	Switch loop II (aa 105–110), which carries the catalytic H108 (H92 in E. coli EF-G; is well resolved in all five structures.	RESULTS
47	56	catalytic	protein_state	Switch loop II (aa 105–110), which carries the catalytic H108 (H92 in E. coli EF-G; is well resolved in all five structures.	RESULTS
57	61	H108	residue_name_number	Switch loop II (aa 105–110), which carries the catalytic H108 (H92 in E. coli EF-G; is well resolved in all five structures.	RESULTS
63	66	H92	residue_name_number	Switch loop II (aa 105–110), which carries the catalytic H108 (H92 in E. coli EF-G; is well resolved in all five structures.	RESULTS
70	77	E. coli	species	Switch loop II (aa 105–110), which carries the catalytic H108 (H92 in E. coli EF-G; is well resolved in all five structures.	RESULTS
78	82	EF-G	protein	Switch loop II (aa 105–110), which carries the catalytic H108 (H92 in E. coli EF-G; is well resolved in all five structures.	RESULTS
113	123	structures	evidence	Switch loop II (aa 105–110), which carries the catalytic H108 (H92 in E. coli EF-G; is well resolved in all five structures.	RESULTS
4	13	histidine	residue_name	The histidine resides next to the backbone of G3028 of the sarcin-ricin loop and near the diphosphate of GDP (Figure 5e).	RESULTS
46	51	G3028	residue_name_number	The histidine resides next to the backbone of G3028 of the sarcin-ricin loop and near the diphosphate of GDP (Figure 5e).	RESULTS
59	76	sarcin-ricin loop	structure_element	The histidine resides next to the backbone of G3028 of the sarcin-ricin loop and near the diphosphate of GDP (Figure 5e).	RESULTS
105	108	GDP	chemical	The histidine resides next to the backbone of G3028 of the sarcin-ricin loop and near the diphosphate of GDP (Figure 5e).	RESULTS
13	26	switch loop I	structure_element	By contrast, switch loop I (aa 50–70 in S. cerevisiae eEF2) is resolved only in Structure I (Figure 5—figure supplement 2).	RESULTS
31	36	50–70	residue_range	By contrast, switch loop I (aa 50–70 in S. cerevisiae eEF2) is resolved only in Structure I (Figure 5—figure supplement 2).	RESULTS
40	53	S. cerevisiae	species	By contrast, switch loop I (aa 50–70 in S. cerevisiae eEF2) is resolved only in Structure I (Figure 5—figure supplement 2).	RESULTS
54	58	eEF2	protein	By contrast, switch loop I (aa 50–70 in S. cerevisiae eEF2) is resolved only in Structure I (Figure 5—figure supplement 2).	RESULTS
80	91	Structure I	evidence	By contrast, switch loop I (aa 50–70 in S. cerevisiae eEF2) is resolved only in Structure I (Figure 5—figure supplement 2).	RESULTS
27	31	loop	structure_element	The N-terminal part of the loop (aa 50–60) is sandwiched between the tip of helix 14 (415CAAA418) of the 18S rRNA of the 40S subunit and helix A (aa 32–42) of eEF2 (Figure 5d).	RESULTS
36	41	50–60	residue_range	The N-terminal part of the loop (aa 50–60) is sandwiched between the tip of helix 14 (415CAAA418) of the 18S rRNA of the 40S subunit and helix A (aa 32–42) of eEF2 (Figure 5d).	RESULTS
76	84	helix 14	structure_element	The N-terminal part of the loop (aa 50–60) is sandwiched between the tip of helix 14 (415CAAA418) of the 18S rRNA of the 40S subunit and helix A (aa 32–42) of eEF2 (Figure 5d).	RESULTS
86	96	415CAAA418	structure_element	The N-terminal part of the loop (aa 50–60) is sandwiched between the tip of helix 14 (415CAAA418) of the 18S rRNA of the 40S subunit and helix A (aa 32–42) of eEF2 (Figure 5d).	RESULTS
105	113	18S rRNA	chemical	The N-terminal part of the loop (aa 50–60) is sandwiched between the tip of helix 14 (415CAAA418) of the 18S rRNA of the 40S subunit and helix A (aa 32–42) of eEF2 (Figure 5d).	RESULTS
121	124	40S	complex_assembly	The N-terminal part of the loop (aa 50–60) is sandwiched between the tip of helix 14 (415CAAA418) of the 18S rRNA of the 40S subunit and helix A (aa 32–42) of eEF2 (Figure 5d).	RESULTS
125	132	subunit	structure_element	The N-terminal part of the loop (aa 50–60) is sandwiched between the tip of helix 14 (415CAAA418) of the 18S rRNA of the 40S subunit and helix A (aa 32–42) of eEF2 (Figure 5d).	RESULTS
125	132	subunit	structure_element	The N-terminal part of the loop (aa 50–60) is sandwiched between the tip of helix 14 (415CAAA418) of the 18S rRNA of the 40S subunit and helix A (aa 32–42) of eEF2 (Figure 5d).	RESULTS
137	144	helix A	structure_element	The N-terminal part of the loop (aa 50–60) is sandwiched between the tip of helix 14 (415CAAA418) of the 18S rRNA of the 40S subunit and helix A (aa 32–42) of eEF2 (Figure 5d).	RESULTS
149	154	32–42	residue_range	The N-terminal part of the loop (aa 50–60) is sandwiched between the tip of helix 14 (415CAAA418) of the 18S rRNA of the 40S subunit and helix A (aa 32–42) of eEF2 (Figure 5d).	RESULTS
159	163	eEF2	protein	The N-terminal part of the loop (aa 50–60) is sandwiched between the tip of helix 14 (415CAAA418) of the 18S rRNA of the 40S subunit and helix A (aa 32–42) of eEF2 (Figure 5d).	RESULTS
0	6	Bulged	protein_state	Bulged A416 interacts with the switch loop in the vicinity of D53.	RESULTS
7	11	A416	residue_name_number	Bulged A416 interacts with the switch loop in the vicinity of D53.	RESULTS
31	42	switch loop	structure_element	Bulged A416 interacts with the switch loop in the vicinity of D53.	RESULTS
62	65	D53	residue_name_number	Bulged A416 interacts with the switch loop in the vicinity of D53.	RESULTS
8	11	GDP	chemical	Next to GDP, the C-terminal part of the switch loop (aa 61–67) adopts a helical fold.	RESULTS
40	51	switch loop	structure_element	Next to GDP, the C-terminal part of the switch loop (aa 61–67) adopts a helical fold.	RESULTS
56	61	61–67	residue_range	Next to GDP, the C-terminal part of the switch loop (aa 61–67) adopts a helical fold.	RESULTS
72	84	helical fold	protein_state	Next to GDP, the C-terminal part of the switch loop (aa 61–67) adopts a helical fold.	RESULTS
30	33	SWI	structure_element	As such, the conformations of SWI and the GTPase center in general are similar to those observed in ribosome-bound EF-Tu and EF-G in the presence of GTP analogs.	RESULTS
42	55	GTPase center	site	As such, the conformations of SWI and the GTPase center in general are similar to those observed in ribosome-bound EF-Tu and EF-G in the presence of GTP analogs.	RESULTS
100	114	ribosome-bound	protein_state	As such, the conformations of SWI and the GTPase center in general are similar to those observed in ribosome-bound EF-Tu and EF-G in the presence of GTP analogs.	RESULTS
115	120	EF-Tu	protein	As such, the conformations of SWI and the GTPase center in general are similar to those observed in ribosome-bound EF-Tu and EF-G in the presence of GTP analogs.	RESULTS
125	129	EF-G	protein	As such, the conformations of SWI and the GTPase center in general are similar to those observed in ribosome-bound EF-Tu and EF-G in the presence of GTP analogs.	RESULTS
137	148	presence of	protein_state	As such, the conformations of SWI and the GTPase center in general are similar to those observed in ribosome-bound EF-Tu and EF-G in the presence of GTP analogs.	RESULTS
149	152	GTP	chemical	As such, the conformations of SWI and the GTPase center in general are similar to those observed in ribosome-bound EF-Tu and EF-G in the presence of GTP analogs.	RESULTS
0	12	Structure II	evidence	Structure II reveals PKI between the body A and P sites and eEF2 partially advanced into the A site	RESULTS
21	24	PKI	structure_element	Structure II reveals PKI between the body A and P sites and eEF2 partially advanced into the A site	RESULTS
37	41	body	structure_element	Structure II reveals PKI between the body A and P sites and eEF2 partially advanced into the A site	RESULTS
42	55	A and P sites	site	Structure II reveals PKI between the body A and P sites and eEF2 partially advanced into the A site	RESULTS
60	64	eEF2	protein	Structure II reveals PKI between the body A and P sites and eEF2 partially advanced into the A site	RESULTS
93	99	A site	site	Structure II reveals PKI between the body A and P sites and eEF2 partially advanced into the A site	RESULTS
3	15	Structure II	evidence	In Structure II, relative to Structure I, PKI is further shifted along the 40S body, traversing ~4 Å toward the P site (Figures 2e, f, and g), while stacking on C1274 at the head A site.	RESULTS
29	40	Structure I	evidence	In Structure II, relative to Structure I, PKI is further shifted along the 40S body, traversing ~4 Å toward the P site (Figures 2e, f, and g), while stacking on C1274 at the head A site.	RESULTS
42	45	PKI	structure_element	In Structure II, relative to Structure I, PKI is further shifted along the 40S body, traversing ~4 Å toward the P site (Figures 2e, f, and g), while stacking on C1274 at the head A site.	RESULTS
75	78	40S	complex_assembly	In Structure II, relative to Structure I, PKI is further shifted along the 40S body, traversing ~4 Å toward the P site (Figures 2e, f, and g), while stacking on C1274 at the head A site.	RESULTS
79	83	body	structure_element	In Structure II, relative to Structure I, PKI is further shifted along the 40S body, traversing ~4 Å toward the P site (Figures 2e, f, and g), while stacking on C1274 at the head A site.	RESULTS
112	118	P site	site	In Structure II, relative to Structure I, PKI is further shifted along the 40S body, traversing ~4 Å toward the P site (Figures 2e, f, and g), while stacking on C1274 at the head A site.	RESULTS
149	157	stacking	bond_interaction	In Structure II, relative to Structure I, PKI is further shifted along the 40S body, traversing ~4 Å toward the P site (Figures 2e, f, and g), while stacking on C1274 at the head A site.	RESULTS
161	166	C1274	residue_name_number	In Structure II, relative to Structure I, PKI is further shifted along the 40S body, traversing ~4 Å toward the P site (Figures 2e, f, and g), while stacking on C1274 at the head A site.	RESULTS
174	178	head	structure_element	In Structure II, relative to Structure I, PKI is further shifted along the 40S body, traversing ~4 Å toward the P site (Figures 2e, f, and g), while stacking on C1274 at the head A site.	RESULTS
179	185	A site	site	In Structure II, relative to Structure I, PKI is further shifted along the 40S body, traversing ~4 Å toward the P site (Figures 2e, f, and g), while stacking on C1274 at the head A site.	RESULTS
35	38	PKI	structure_element	Thus, the intermediate position of PKI is possible due to a large swivel of the head relative to the body, which brings the head A site close to the body P site.	RESULTS
80	84	head	structure_element	Thus, the intermediate position of PKI is possible due to a large swivel of the head relative to the body, which brings the head A site close to the body P site.	RESULTS
101	105	body	structure_element	Thus, the intermediate position of PKI is possible due to a large swivel of the head relative to the body, which brings the head A site close to the body P site.	RESULTS
124	128	head	structure_element	Thus, the intermediate position of PKI is possible due to a large swivel of the head relative to the body, which brings the head A site close to the body P site.	RESULTS
129	135	A site	site	Thus, the intermediate position of PKI is possible due to a large swivel of the head relative to the body, which brings the head A site close to the body P site.	RESULTS
149	153	body	structure_element	Thus, the intermediate position of PKI is possible due to a large swivel of the head relative to the body, which brings the head A site close to the body P site.	RESULTS
154	160	P site	site	Thus, the intermediate position of PKI is possible due to a large swivel of the head relative to the body, which brings the head A site close to the body P site.	RESULTS
7	9	IV	structure_element	Domain IV of eEF2 is further entrenched in the A site by ~3 Å relative to the body and ~8 Å relative to the head, preserving its interactions with PKI.	RESULTS
13	17	eEF2	protein	Domain IV of eEF2 is further entrenched in the A site by ~3 Å relative to the body and ~8 Å relative to the head, preserving its interactions with PKI.	RESULTS
47	53	A site	site	Domain IV of eEF2 is further entrenched in the A site by ~3 Å relative to the body and ~8 Å relative to the head, preserving its interactions with PKI.	RESULTS
78	82	body	structure_element	Domain IV of eEF2 is further entrenched in the A site by ~3 Å relative to the body and ~8 Å relative to the head, preserving its interactions with PKI.	RESULTS
108	112	head	structure_element	Domain IV of eEF2 is further entrenched in the A site by ~3 Å relative to the body and ~8 Å relative to the head, preserving its interactions with PKI.	RESULTS
147	150	PKI	structure_element	Domain IV of eEF2 is further entrenched in the A site by ~3 Å relative to the body and ~8 Å relative to the head, preserving its interactions with PKI.	RESULTS
4	19	decoding center	site	The decoding center residues A1755 and A1756 are rearranged to pack inside helix 44, making room for eEF2.	RESULTS
29	34	A1755	residue_name_number	The decoding center residues A1755 and A1756 are rearranged to pack inside helix 44, making room for eEF2.	RESULTS
39	44	A1756	residue_name_number	The decoding center residues A1755 and A1756 are rearranged to pack inside helix 44, making room for eEF2.	RESULTS
75	83	helix 44	structure_element	The decoding center residues A1755 and A1756 are rearranged to pack inside helix 44, making room for eEF2.	RESULTS
101	105	eEF2	protein	The decoding center residues A1755 and A1756 are rearranged to pack inside helix 44, making room for eEF2.	RESULTS
21	36	decoding center	site	This conformation of decoding center residues is also observed in the absence of A-site ligands.	RESULTS
70	80	absence of	protein_state	This conformation of decoding center residues is also observed in the absence of A-site ligands.	RESULTS
81	87	A-site	site	This conformation of decoding center residues is also observed in the absence of A-site ligands.	RESULTS
4	18	head interface	site	The head interface of domain IV interacts with the 40S head (Figure 6a).	RESULTS
29	31	IV	structure_element	The head interface of domain IV interacts with the 40S head (Figure 6a).	RESULTS
51	54	40S	complex_assembly	The head interface of domain IV interacts with the 40S head (Figure 6a).	RESULTS
55	59	head	structure_element	The head interface of domain IV interacts with the 40S head (Figure 6a).	RESULTS
8	34	positively charged surface	site	Here, a positively charged surface of eEF2, formed by K613, R617 and R631 contacts the phosphate backbone of helix 33 (Figures 6c; see also Figure 6—figure supplement 1).	RESULTS
38	42	eEF2	protein	Here, a positively charged surface of eEF2, formed by K613, R617 and R631 contacts the phosphate backbone of helix 33 (Figures 6c; see also Figure 6—figure supplement 1).	RESULTS
54	58	K613	residue_name_number	Here, a positively charged surface of eEF2, formed by K613, R617 and R631 contacts the phosphate backbone of helix 33 (Figures 6c; see also Figure 6—figure supplement 1).	RESULTS
60	64	R617	residue_name_number	Here, a positively charged surface of eEF2, formed by K613, R617 and R631 contacts the phosphate backbone of helix 33 (Figures 6c; see also Figure 6—figure supplement 1).	RESULTS
69	73	R631	residue_name_number	Here, a positively charged surface of eEF2, formed by K613, R617 and R631 contacts the phosphate backbone of helix 33 (Figures 6c; see also Figure 6—figure supplement 1).	RESULTS
109	117	helix 33	structure_element	Here, a positively charged surface of eEF2, formed by K613, R617 and R631 contacts the phosphate backbone of helix 33 (Figures 6c; see also Figure 6—figure supplement 1).	RESULTS
0	13	Structure III	evidence	Structure III represents a highly bent IRES with PKI captured between the head A and P sites	RESULTS
27	38	highly bent	protein_state	Structure III represents a highly bent IRES with PKI captured between the head A and P sites	RESULTS
39	43	IRES	site	Structure III represents a highly bent IRES with PKI captured between the head A and P sites	RESULTS
49	52	PKI	structure_element	Structure III represents a highly bent IRES with PKI captured between the head A and P sites	RESULTS
74	78	head	structure_element	Structure III represents a highly bent IRES with PKI captured between the head A and P sites	RESULTS
79	92	A and P sites	site	Structure III represents a highly bent IRES with PKI captured between the head A and P sites	RESULTS
28	32	head	structure_element	Consistent with the similar head swivels in Structure III and Structure II, relative positions of the 40S head A site and body P site remain as in Structure II.	RESULTS
44	57	Structure III	evidence	Consistent with the similar head swivels in Structure III and Structure II, relative positions of the 40S head A site and body P site remain as in Structure II.	RESULTS
62	74	Structure II	evidence	Consistent with the similar head swivels in Structure III and Structure II, relative positions of the 40S head A site and body P site remain as in Structure II.	RESULTS
102	105	40S	complex_assembly	Consistent with the similar head swivels in Structure III and Structure II, relative positions of the 40S head A site and body P site remain as in Structure II.	RESULTS
106	110	head	structure_element	Consistent with the similar head swivels in Structure III and Structure II, relative positions of the 40S head A site and body P site remain as in Structure II.	RESULTS
111	117	A site	site	Consistent with the similar head swivels in Structure III and Structure II, relative positions of the 40S head A site and body P site remain as in Structure II.	RESULTS
122	126	body	structure_element	Consistent with the similar head swivels in Structure III and Structure II, relative positions of the 40S head A site and body P site remain as in Structure II.	RESULTS
127	133	P site	site	Consistent with the similar head swivels in Structure III and Structure II, relative positions of the 40S head A site and body P site remain as in Structure II.	RESULTS
147	159	Structure II	evidence	Consistent with the similar head swivels in Structure III and Structure II, relative positions of the 40S head A site and body P site remain as in Structure II.	RESULTS
15	25	structures	evidence	Among the five structures, the PKI domain is least ordered in Structure III and lacks density for SL3.	RESULTS
31	34	PKI	structure_element	Among the five structures, the PKI domain is least ordered in Structure III and lacks density for SL3.	RESULTS
62	75	Structure III	evidence	Among the five structures, the PKI domain is least ordered in Structure III and lacks density for SL3.	RESULTS
86	93	density	evidence	Among the five structures, the PKI domain is least ordered in Structure III and lacks density for SL3.	RESULTS
98	101	SL3	structure_element	Among the five structures, the PKI domain is least ordered in Structure III and lacks density for SL3.	RESULTS
4	7	map	evidence	The map allows placement of PKI at the body P site (Figure 1—figure supplement 3).	RESULTS
28	31	PKI	structure_element	The map allows placement of PKI at the body P site (Figure 1—figure supplement 3).	RESULTS
39	43	body	structure_element	The map allows placement of PKI at the body P site (Figure 1—figure supplement 3).	RESULTS
44	50	P site	site	The map allows placement of PKI at the body P site (Figure 1—figure supplement 3).	RESULTS
9	22	Structure III	evidence	Thus, in Structure III, PKI has translocated along the 40S body, but the head remains fully swiveled so that PKI is between the head A and P sites.	RESULTS
24	27	PKI	structure_element	Thus, in Structure III, PKI has translocated along the 40S body, but the head remains fully swiveled so that PKI is between the head A and P sites.	RESULTS
55	58	40S	complex_assembly	Thus, in Structure III, PKI has translocated along the 40S body, but the head remains fully swiveled so that PKI is between the head A and P sites.	RESULTS
59	63	body	structure_element	Thus, in Structure III, PKI has translocated along the 40S body, but the head remains fully swiveled so that PKI is between the head A and P sites.	RESULTS
73	77	head	structure_element	Thus, in Structure III, PKI has translocated along the 40S body, but the head remains fully swiveled so that PKI is between the head A and P sites.	RESULTS
86	100	fully swiveled	protein_state	Thus, in Structure III, PKI has translocated along the 40S body, but the head remains fully swiveled so that PKI is between the head A and P sites.	RESULTS
109	112	PKI	structure_element	Thus, in Structure III, PKI has translocated along the 40S body, but the head remains fully swiveled so that PKI is between the head A and P sites.	RESULTS
128	132	head	structure_element	Thus, in Structure III, PKI has translocated along the 40S body, but the head remains fully swiveled so that PKI is between the head A and P sites.	RESULTS
133	146	A and P sites	site	Thus, in Structure III, PKI has translocated along the 40S body, but the head remains fully swiveled so that PKI is between the head A and P sites.	RESULTS
24	27	map	evidence	Lower resolution of the map in this region suggests that PKI is somewhat destabilized in the vicinity of the body P site in the absence of stacking with the foundations of the head A site (C1274) or P site (U1191).	RESULTS
57	60	PKI	structure_element	Lower resolution of the map in this region suggests that PKI is somewhat destabilized in the vicinity of the body P site in the absence of stacking with the foundations of the head A site (C1274) or P site (U1191).	RESULTS
109	113	body	structure_element	Lower resolution of the map in this region suggests that PKI is somewhat destabilized in the vicinity of the body P site in the absence of stacking with the foundations of the head A site (C1274) or P site (U1191).	RESULTS
114	120	P site	site	Lower resolution of the map in this region suggests that PKI is somewhat destabilized in the vicinity of the body P site in the absence of stacking with the foundations of the head A site (C1274) or P site (U1191).	RESULTS
128	138	absence of	protein_state	Lower resolution of the map in this region suggests that PKI is somewhat destabilized in the vicinity of the body P site in the absence of stacking with the foundations of the head A site (C1274) or P site (U1191).	RESULTS
139	147	stacking	bond_interaction	Lower resolution of the map in this region suggests that PKI is somewhat destabilized in the vicinity of the body P site in the absence of stacking with the foundations of the head A site (C1274) or P site (U1191).	RESULTS
176	180	head	structure_element	Lower resolution of the map in this region suggests that PKI is somewhat destabilized in the vicinity of the body P site in the absence of stacking with the foundations of the head A site (C1274) or P site (U1191).	RESULTS
181	187	A site	site	Lower resolution of the map in this region suggests that PKI is somewhat destabilized in the vicinity of the body P site in the absence of stacking with the foundations of the head A site (C1274) or P site (U1191).	RESULTS
189	194	C1274	residue_name_number	Lower resolution of the map in this region suggests that PKI is somewhat destabilized in the vicinity of the body P site in the absence of stacking with the foundations of the head A site (C1274) or P site (U1191).	RESULTS
199	205	P site	site	Lower resolution of the map in this region suggests that PKI is somewhat destabilized in the vicinity of the body P site in the absence of stacking with the foundations of the head A site (C1274) or P site (U1191).	RESULTS
207	212	U1191	residue_name_number	Lower resolution of the map in this region suggests that PKI is somewhat destabilized in the vicinity of the body P site in the absence of stacking with the foundations of the head A site (C1274) or P site (U1191).	RESULTS
16	20	eEF2	protein	The position of eEF2 is similar to that in Structure II.	RESULTS
43	55	Structure II	evidence	The position of eEF2 is similar to that in Structure II.	RESULTS
0	12	Structure IV	evidence	Structure IV represents a highly bent IRES with PKI partially accommodated in the P site	RESULTS
26	37	highly bent	protein_state	Structure IV represents a highly bent IRES with PKI partially accommodated in the P site	RESULTS
38	42	IRES	site	Structure IV represents a highly bent IRES with PKI partially accommodated in the P site	RESULTS
48	51	PKI	structure_element	Structure IV represents a highly bent IRES with PKI partially accommodated in the P site	RESULTS
82	88	P site	site	Structure IV represents a highly bent IRES with PKI partially accommodated in the P site	RESULTS
3	15	Structure IV	evidence	In Structure IV, the 40S subunit is almost non-rotated relative to the 60S subunit, and the 40S head is mid-swiveled.	RESULTS
21	24	40S	complex_assembly	In Structure IV, the 40S subunit is almost non-rotated relative to the 60S subunit, and the 40S head is mid-swiveled.	RESULTS
25	32	subunit	structure_element	In Structure IV, the 40S subunit is almost non-rotated relative to the 60S subunit, and the 40S head is mid-swiveled.	RESULTS
25	32	subunit	structure_element	In Structure IV, the 40S subunit is almost non-rotated relative to the 60S subunit, and the 40S head is mid-swiveled.	RESULTS
43	54	non-rotated	protein_state	In Structure IV, the 40S subunit is almost non-rotated relative to the 60S subunit, and the 40S head is mid-swiveled.	RESULTS
71	74	60S	complex_assembly	In Structure IV, the 40S subunit is almost non-rotated relative to the 60S subunit, and the 40S head is mid-swiveled.	RESULTS
75	82	subunit	structure_element	In Structure IV, the 40S subunit is almost non-rotated relative to the 60S subunit, and the 40S head is mid-swiveled.	RESULTS
92	95	40S	complex_assembly	In Structure IV, the 40S subunit is almost non-rotated relative to the 60S subunit, and the 40S head is mid-swiveled.	RESULTS
96	100	head	structure_element	In Structure IV, the 40S subunit is almost non-rotated relative to the 60S subunit, and the 40S head is mid-swiveled.	RESULTS
104	116	mid-swiveled	protein_state	In Structure IV, the 40S subunit is almost non-rotated relative to the 60S subunit, and the 40S head is mid-swiveled.	RESULTS
17	21	head	structure_element	Unwinding of the head moves the head P-site residue U1191 and body P-site residue C1637 closer together, resulting in a partially restored 40S P site.	RESULTS
32	36	head	structure_element	Unwinding of the head moves the head P-site residue U1191 and body P-site residue C1637 closer together, resulting in a partially restored 40S P site.	RESULTS
37	43	P-site	site	Unwinding of the head moves the head P-site residue U1191 and body P-site residue C1637 closer together, resulting in a partially restored 40S P site.	RESULTS
52	57	U1191	residue_name_number	Unwinding of the head moves the head P-site residue U1191 and body P-site residue C1637 closer together, resulting in a partially restored 40S P site.	RESULTS
62	66	body	structure_element	Unwinding of the head moves the head P-site residue U1191 and body P-site residue C1637 closer together, resulting in a partially restored 40S P site.	RESULTS
67	73	P-site	site	Unwinding of the head moves the head P-site residue U1191 and body P-site residue C1637 closer together, resulting in a partially restored 40S P site.	RESULTS
82	87	C1637	residue_name_number	Unwinding of the head moves the head P-site residue U1191 and body P-site residue C1637 closer together, resulting in a partially restored 40S P site.	RESULTS
139	142	40S	complex_assembly	Unwinding of the head moves the head P-site residue U1191 and body P-site residue C1637 closer together, resulting in a partially restored 40S P site.	RESULTS
143	149	P site	site	Unwinding of the head moves the head P-site residue U1191 and body P-site residue C1637 closer together, resulting in a partially restored 40S P site.	RESULTS
8	13	C1637	residue_name_number	Whereas C1637 forms a stacking platform for the last base pair of PKI, U1191 does not yet stack on PKI because the head remains partially swiveled.	RESULTS
22	39	stacking platform	site	Whereas C1637 forms a stacking platform for the last base pair of PKI, U1191 does not yet stack on PKI because the head remains partially swiveled.	RESULTS
66	69	PKI	structure_element	Whereas C1637 forms a stacking platform for the last base pair of PKI, U1191 does not yet stack on PKI because the head remains partially swiveled.	RESULTS
71	76	U1191	residue_name_number	Whereas C1637 forms a stacking platform for the last base pair of PKI, U1191 does not yet stack on PKI because the head remains partially swiveled.	RESULTS
90	95	stack	bond_interaction	Whereas C1637 forms a stacking platform for the last base pair of PKI, U1191 does not yet stack on PKI because the head remains partially swiveled.	RESULTS
99	102	PKI	structure_element	Whereas C1637 forms a stacking platform for the last base pair of PKI, U1191 does not yet stack on PKI because the head remains partially swiveled.	RESULTS
115	119	head	structure_element	Whereas C1637 forms a stacking platform for the last base pair of PKI, U1191 does not yet stack on PKI because the head remains partially swiveled.	RESULTS
13	16	PKI	structure_element	This renders PKI partially accommodated in the P site (Figure 2g).	RESULTS
47	53	P site	site	This renders PKI partially accommodated in the P site (Figure 2g).	RESULTS
17	20	40S	complex_assembly	Unwinding of the 40S head also positions the head A site closer to the body A site.	RESULTS
21	25	head	structure_element	Unwinding of the 40S head also positions the head A site closer to the body A site.	RESULTS
45	49	head	structure_element	Unwinding of the 40S head also positions the head A site closer to the body A site.	RESULTS
50	56	A site	site	Unwinding of the 40S head also positions the head A site closer to the body A site.	RESULTS
71	75	body	structure_element	Unwinding of the 40S head also positions the head A site closer to the body A site.	RESULTS
76	82	A site	site	Unwinding of the 40S head also positions the head A site closer to the body A site.	RESULTS
34	38	eEF2	protein	This results in rearrangements of eEF2 interactions with the head, allowing eEF2 to advance further into the A site.	RESULTS
61	65	head	structure_element	This results in rearrangements of eEF2 interactions with the head, allowing eEF2 to advance further into the A site.	RESULTS
76	80	eEF2	protein	This results in rearrangements of eEF2 interactions with the head, allowing eEF2 to advance further into the A site.	RESULTS
109	115	A site	site	This results in rearrangements of eEF2 interactions with the head, allowing eEF2 to advance further into the A site.	RESULTS
17	43	head-interacting interface	site	To this end, the head-interacting interface of domain IV slides along the surface of the head by 5 Å. Helix A of domain IV is positioned next to the backbone of h34, with positively charged residues K613, R617 and R631 rearranged from the backbone of h33 (Figure 6c; see also Figure 6—figure supplement 1).	RESULTS
54	56	IV	structure_element	To this end, the head-interacting interface of domain IV slides along the surface of the head by 5 Å. Helix A of domain IV is positioned next to the backbone of h34, with positively charged residues K613, R617 and R631 rearranged from the backbone of h33 (Figure 6c; see also Figure 6—figure supplement 1).	RESULTS
89	93	head	structure_element	To this end, the head-interacting interface of domain IV slides along the surface of the head by 5 Å. Helix A of domain IV is positioned next to the backbone of h34, with positively charged residues K613, R617 and R631 rearranged from the backbone of h33 (Figure 6c; see also Figure 6—figure supplement 1).	RESULTS
102	109	Helix A	structure_element	To this end, the head-interacting interface of domain IV slides along the surface of the head by 5 Å. Helix A of domain IV is positioned next to the backbone of h34, with positively charged residues K613, R617 and R631 rearranged from the backbone of h33 (Figure 6c; see also Figure 6—figure supplement 1).	RESULTS
120	122	IV	structure_element	To this end, the head-interacting interface of domain IV slides along the surface of the head by 5 Å. Helix A of domain IV is positioned next to the backbone of h34, with positively charged residues K613, R617 and R631 rearranged from the backbone of h33 (Figure 6c; see also Figure 6—figure supplement 1).	RESULTS
161	164	h34	structure_element	To this end, the head-interacting interface of domain IV slides along the surface of the head by 5 Å. Helix A of domain IV is positioned next to the backbone of h34, with positively charged residues K613, R617 and R631 rearranged from the backbone of h33 (Figure 6c; see also Figure 6—figure supplement 1).	RESULTS
199	203	K613	residue_name_number	To this end, the head-interacting interface of domain IV slides along the surface of the head by 5 Å. Helix A of domain IV is positioned next to the backbone of h34, with positively charged residues K613, R617 and R631 rearranged from the backbone of h33 (Figure 6c; see also Figure 6—figure supplement 1).	RESULTS
205	209	R617	residue_name_number	To this end, the head-interacting interface of domain IV slides along the surface of the head by 5 Å. Helix A of domain IV is positioned next to the backbone of h34, with positively charged residues K613, R617 and R631 rearranged from the backbone of h33 (Figure 6c; see also Figure 6—figure supplement 1).	RESULTS
214	218	R631	residue_name_number	To this end, the head-interacting interface of domain IV slides along the surface of the head by 5 Å. Helix A of domain IV is positioned next to the backbone of h34, with positively charged residues K613, R617 and R631 rearranged from the backbone of h33 (Figure 6c; see also Figure 6—figure supplement 1).	RESULTS
251	254	h33	structure_element	To this end, the head-interacting interface of domain IV slides along the surface of the head by 5 Å. Helix A of domain IV is positioned next to the backbone of h34, with positively charged residues K613, R617 and R631 rearranged from the backbone of h33 (Figure 6c; see also Figure 6—figure supplement 1).	RESULTS
0	11	Structure V	evidence	Structure V represents an extended IRES with PKI fully accommodated in the P site and domain IV of eEF2 in the A site	RESULTS
26	34	extended	protein_state	Structure V represents an extended IRES with PKI fully accommodated in the P site and domain IV of eEF2 in the A site	RESULTS
35	39	IRES	site	Structure V represents an extended IRES with PKI fully accommodated in the P site and domain IV of eEF2 in the A site	RESULTS
45	48	PKI	structure_element	Structure V represents an extended IRES with PKI fully accommodated in the P site and domain IV of eEF2 in the A site	RESULTS
75	81	P site	site	Structure V represents an extended IRES with PKI fully accommodated in the P site and domain IV of eEF2 in the A site	RESULTS
93	95	IV	structure_element	Structure V represents an extended IRES with PKI fully accommodated in the P site and domain IV of eEF2 in the A site	RESULTS
99	103	eEF2	protein	Structure V represents an extended IRES with PKI fully accommodated in the P site and domain IV of eEF2 in the A site	RESULTS
111	117	A site	site	Structure V represents an extended IRES with PKI fully accommodated in the P site and domain IV of eEF2 in the A site	RESULTS
7	25	nearly non-rotated	protein_state	In the nearly non-rotated and non-swiveled ribosome conformation in Structure V closely resembling that of the post-translocation 80S•2tRNA•mRNA complex, PKI is fully accommodated in the P site.	RESULTS
30	42	non-swiveled	protein_state	In the nearly non-rotated and non-swiveled ribosome conformation in Structure V closely resembling that of the post-translocation 80S•2tRNA•mRNA complex, PKI is fully accommodated in the P site.	RESULTS
43	51	ribosome	complex_assembly	In the nearly non-rotated and non-swiveled ribosome conformation in Structure V closely resembling that of the post-translocation 80S•2tRNA•mRNA complex, PKI is fully accommodated in the P site.	RESULTS
68	79	Structure V	evidence	In the nearly non-rotated and non-swiveled ribosome conformation in Structure V closely resembling that of the post-translocation 80S•2tRNA•mRNA complex, PKI is fully accommodated in the P site.	RESULTS
111	129	post-translocation	protein_state	In the nearly non-rotated and non-swiveled ribosome conformation in Structure V closely resembling that of the post-translocation 80S•2tRNA•mRNA complex, PKI is fully accommodated in the P site.	RESULTS
130	144	80S•2tRNA•mRNA	complex_assembly	In the nearly non-rotated and non-swiveled ribosome conformation in Structure V closely resembling that of the post-translocation 80S•2tRNA•mRNA complex, PKI is fully accommodated in the P site.	RESULTS
154	157	PKI	structure_element	In the nearly non-rotated and non-swiveled ribosome conformation in Structure V closely resembling that of the post-translocation 80S•2tRNA•mRNA complex, PKI is fully accommodated in the P site.	RESULTS
187	193	P site	site	In the nearly non-rotated and non-swiveled ribosome conformation in Structure V closely resembling that of the post-translocation 80S•2tRNA•mRNA complex, PKI is fully accommodated in the P site.	RESULTS
4	30	codon-anticodon–like helix	structure_element	The codon-anticodon–like helix is stacked on P-site residues U1191 and C1637 (Figure 3d), analogous to stacking of the tRNA-mRNA helix (Figure 3e).	RESULTS
45	51	P-site	site	The codon-anticodon–like helix is stacked on P-site residues U1191 and C1637 (Figure 3d), analogous to stacking of the tRNA-mRNA helix (Figure 3e).	RESULTS
61	66	U1191	residue_name_number	The codon-anticodon–like helix is stacked on P-site residues U1191 and C1637 (Figure 3d), analogous to stacking of the tRNA-mRNA helix (Figure 3e).	RESULTS
71	76	C1637	residue_name_number	The codon-anticodon–like helix is stacked on P-site residues U1191 and C1637 (Figure 3d), analogous to stacking of the tRNA-mRNA helix (Figure 3e).	RESULTS
103	111	stacking	bond_interaction	The codon-anticodon–like helix is stacked on P-site residues U1191 and C1637 (Figure 3d), analogous to stacking of the tRNA-mRNA helix (Figure 3e).	RESULTS
119	128	tRNA-mRNA	complex_assembly	The codon-anticodon–like helix is stacked on P-site residues U1191 and C1637 (Figure 3d), analogous to stacking of the tRNA-mRNA helix (Figure 3e).	RESULTS
129	134	helix	structure_element	The codon-anticodon–like helix is stacked on P-site residues U1191 and C1637 (Figure 3d), analogous to stacking of the tRNA-mRNA helix (Figure 3e).	RESULTS
35	39	eEF2	protein	A notable conformational change in eEF2 from that in the preceding Structures is visible in the position of domain III, which contacts uS12 (Figure 6d).	RESULTS
67	77	Structures	evidence	A notable conformational change in eEF2 from that in the preceding Structures is visible in the position of domain III, which contacts uS12 (Figure 6d).	RESULTS
115	118	III	structure_element	A notable conformational change in eEF2 from that in the preceding Structures is visible in the position of domain III, which contacts uS12 (Figure 6d).	RESULTS
135	139	uS12	protein	A notable conformational change in eEF2 from that in the preceding Structures is visible in the position of domain III, which contacts uS12 (Figure 6d).	RESULTS
3	14	Structure V	evidence	In Structure V, protein uS12 is shifted along with the 40S body as a result of intersubunit rotation.	RESULTS
24	28	uS12	protein	In Structure V, protein uS12 is shifted along with the 40S body as a result of intersubunit rotation.	RESULTS
55	58	40S	complex_assembly	In Structure V, protein uS12 is shifted along with the 40S body as a result of intersubunit rotation.	RESULTS
59	63	body	structure_element	In Structure V, protein uS12 is shifted along with the 40S body as a result of intersubunit rotation.	RESULTS
18	22	uS12	protein	In this position, uS12 forms extensive interactions with eEF2 domains II and III.	RESULTS
57	61	eEF2	protein	In this position, uS12 forms extensive interactions with eEF2 domains II and III.	RESULTS
70	72	II	structure_element	In this position, uS12 forms extensive interactions with eEF2 domains II and III.	RESULTS
77	80	III	structure_element	In this position, uS12 forms extensive interactions with eEF2 domains II and III.	RESULTS
18	33	C-terminal tail	structure_element	Specifically, the C-terminal tail of uS12 packs against the β-barrel of domain II, while the β-barrel of uS12 packs against helix A of domain III.	RESULTS
37	41	uS12	protein	Specifically, the C-terminal tail of uS12 packs against the β-barrel of domain II, while the β-barrel of uS12 packs against helix A of domain III.	RESULTS
60	68	β-barrel	structure_element	Specifically, the C-terminal tail of uS12 packs against the β-barrel of domain II, while the β-barrel of uS12 packs against helix A of domain III.	RESULTS
79	81	II	structure_element	Specifically, the C-terminal tail of uS12 packs against the β-barrel of domain II, while the β-barrel of uS12 packs against helix A of domain III.	RESULTS
93	101	β-barrel	structure_element	Specifically, the C-terminal tail of uS12 packs against the β-barrel of domain II, while the β-barrel of uS12 packs against helix A of domain III.	RESULTS
105	109	uS12	protein	Specifically, the C-terminal tail of uS12 packs against the β-barrel of domain II, while the β-barrel of uS12 packs against helix A of domain III.	RESULTS
124	131	helix A	structure_element	Specifically, the C-terminal tail of uS12 packs against the β-barrel of domain II, while the β-barrel of uS12 packs against helix A of domain III.	RESULTS
142	145	III	structure_element	Specifically, the C-terminal tail of uS12 packs against the β-barrel of domain II, while the β-barrel of uS12 packs against helix A of domain III.	RESULTS
23	30	helix A	structure_element	This shifts the tip of helix A of domain III (at aa 500) by ~5 Å (relative to that in Structure I) toward domain I. Although domain III remains in contact with domain V, the shift occurs in the direction that could eventually disconnect the β-platforms of these domains.	RESULTS
41	44	III	structure_element	This shifts the tip of helix A of domain III (at aa 500) by ~5 Å (relative to that in Structure I) toward domain I. Although domain III remains in contact with domain V, the shift occurs in the direction that could eventually disconnect the β-platforms of these domains.	RESULTS
52	55	500	residue_number	This shifts the tip of helix A of domain III (at aa 500) by ~5 Å (relative to that in Structure I) toward domain I. Although domain III remains in contact with domain V, the shift occurs in the direction that could eventually disconnect the β-platforms of these domains.	RESULTS
86	97	Structure I	evidence	This shifts the tip of helix A of domain III (at aa 500) by ~5 Å (relative to that in Structure I) toward domain I. Although domain III remains in contact with domain V, the shift occurs in the direction that could eventually disconnect the β-platforms of these domains.	RESULTS
113	114	I	structure_element	This shifts the tip of helix A of domain III (at aa 500) by ~5 Å (relative to that in Structure I) toward domain I. Although domain III remains in contact with domain V, the shift occurs in the direction that could eventually disconnect the β-platforms of these domains.	RESULTS
132	135	III	structure_element	This shifts the tip of helix A of domain III (at aa 500) by ~5 Å (relative to that in Structure I) toward domain I. Although domain III remains in contact with domain V, the shift occurs in the direction that could eventually disconnect the β-platforms of these domains.	RESULTS
167	168	V	structure_element	This shifts the tip of helix A of domain III (at aa 500) by ~5 Å (relative to that in Structure I) toward domain I. Although domain III remains in contact with domain V, the shift occurs in the direction that could eventually disconnect the β-platforms of these domains.	RESULTS
241	252	β-platforms	structure_element	This shifts the tip of helix A of domain III (at aa 500) by ~5 Å (relative to that in Structure I) toward domain I. Although domain III remains in contact with domain V, the shift occurs in the direction that could eventually disconnect the β-platforms of these domains.	RESULTS
7	9	IV	structure_element	Domain IV of eEF2 is fully accommodated in the A site.	RESULTS
13	17	eEF2	protein	Domain IV of eEF2 is fully accommodated in the A site.	RESULTS
47	53	A site	site	Domain IV of eEF2 is fully accommodated in the A site.	RESULTS
23	41	open reading frame	structure_element	The first codon of the open reading frame is also positioned in the A site, with bases exposed toward eEF2 (Figure 7), resembling the conformations of the A-site codons in EF-G-bound 70S complexes.	RESULTS
68	74	A site	site	The first codon of the open reading frame is also positioned in the A site, with bases exposed toward eEF2 (Figure 7), resembling the conformations of the A-site codons in EF-G-bound 70S complexes.	RESULTS
102	106	eEF2	protein	The first codon of the open reading frame is also positioned in the A site, with bases exposed toward eEF2 (Figure 7), resembling the conformations of the A-site codons in EF-G-bound 70S complexes.	RESULTS
155	161	A-site	site	The first codon of the open reading frame is also positioned in the A site, with bases exposed toward eEF2 (Figure 7), resembling the conformations of the A-site codons in EF-G-bound 70S complexes.	RESULTS
172	182	EF-G-bound	protein_state	The first codon of the open reading frame is also positioned in the A site, with bases exposed toward eEF2 (Figure 7), resembling the conformations of the A-site codons in EF-G-bound 70S complexes.	RESULTS
183	186	70S	complex_assembly	The first codon of the open reading frame is also positioned in the A site, with bases exposed toward eEF2 (Figure 7), resembling the conformations of the A-site codons in EF-G-bound 70S complexes.	RESULTS
20	30	Structures	evidence	As in the preceding Structures, the histidine-diphthamide tip is bound in the minor groove of the P-site codon-anticodon helix.	RESULTS
36	61	histidine-diphthamide tip	site	As in the preceding Structures, the histidine-diphthamide tip is bound in the minor groove of the P-site codon-anticodon helix.	RESULTS
65	73	bound in	protein_state	As in the preceding Structures, the histidine-diphthamide tip is bound in the minor groove of the P-site codon-anticodon helix.	RESULTS
78	90	minor groove	site	As in the preceding Structures, the histidine-diphthamide tip is bound in the minor groove of the P-site codon-anticodon helix.	RESULTS
98	104	P-site	site	As in the preceding Structures, the histidine-diphthamide tip is bound in the minor groove of the P-site codon-anticodon helix.	RESULTS
105	126	codon-anticodon helix	structure_element	As in the preceding Structures, the histidine-diphthamide tip is bound in the minor groove of the P-site codon-anticodon helix.	RESULTS
0	7	Diph699	ptm	Diph699 slightly rearranges, relative to that in Structure I (Figure 7), and interacts with four out of six codon-anticodon nucleotides.	RESULTS
49	60	Structure I	evidence	Diph699 slightly rearranges, relative to that in Structure I (Figure 7), and interacts with four out of six codon-anticodon nucleotides.	RESULTS
31	36	G6907	residue_name_number	The imidazole moiety stacks on G6907 (corresponding to nt 36 in the tRNA anticodon) and hydrogen bonds with O2’ of G6906 (nt 35 of tRNA).	RESULTS
68	72	tRNA	chemical	The imidazole moiety stacks on G6907 (corresponding to nt 36 in the tRNA anticodon) and hydrogen bonds with O2’ of G6906 (nt 35 of tRNA).	RESULTS
88	102	hydrogen bonds	bond_interaction	The imidazole moiety stacks on G6907 (corresponding to nt 36 in the tRNA anticodon) and hydrogen bonds with O2’ of G6906 (nt 35 of tRNA).	RESULTS
115	120	G6906	residue_name_number	The imidazole moiety stacks on G6907 (corresponding to nt 36 in the tRNA anticodon) and hydrogen bonds with O2’ of G6906 (nt 35 of tRNA).	RESULTS
131	135	tRNA	chemical	The imidazole moiety stacks on G6907 (corresponding to nt 36 in the tRNA anticodon) and hydrogen bonds with O2’ of G6906 (nt 35 of tRNA).	RESULTS
17	28	diphthamide	ptm	The amide at the diphthamide end interacts with N2 of G6906 and O2 and O2’ of C6951 (corresponding to nt 2 of the codon).	RESULTS
54	59	G6906	residue_name_number	The amide at the diphthamide end interacts with N2 of G6906 and O2 and O2’ of C6951 (corresponding to nt 2 of the codon).	RESULTS
78	83	C6951	residue_name_number	The amide at the diphthamide end interacts with N2 of G6906 and O2 and O2’ of C6951 (corresponding to nt 2 of the codon).	RESULTS
58	63	C6952	residue_name_number	The trimethylamino-group is positioned over the ribose of C6952 (codon nt 3).	RESULTS
0	4	IRES	site	IRES translocation mechanism	DISCUSS
42	52	initiation	protein_state	Animation showing the transition from the initiation 80S•TSV IRES structures (Koh et al., 2014) to eEF2-bound Structures I through V (this work).	FIG
53	65	80S•TSV IRES	complex_assembly	Animation showing the transition from the initiation 80S•TSV IRES structures (Koh et al., 2014) to eEF2-bound Structures I through V (this work).	FIG
66	76	structures	evidence	Animation showing the transition from the initiation 80S•TSV IRES structures (Koh et al., 2014) to eEF2-bound Structures I through V (this work).	FIG
99	109	eEF2-bound	protein_state	Animation showing the transition from the initiation 80S•TSV IRES structures (Koh et al., 2014) to eEF2-bound Structures I through V (this work).	FIG
110	132	Structures I through V	evidence	Animation showing the transition from the initiation 80S•TSV IRES structures (Koh et al., 2014) to eEF2-bound Structures I through V (this work).	FIG
80	84	head	structure_element	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
92	95	40S	complex_assembly	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
96	103	subunit	structure_element	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
185	188	40S	complex_assembly	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
189	196	subunit	structure_element	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
207	210	40S	complex_assembly	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
211	215	head	structure_element	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
318	321	40S	complex_assembly	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
322	329	subunit	structure_element	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
358	373	decoding center	site	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
375	381	A site	site	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
391	397	P site	site	Four views (scenes) are shown: (1) A view down the intersubunit space, with the head of the 40S subunit oriented toward a viewer, as in Figure 1a; (2) A view at the solvent side of the 40S subunit, with the 40S head shown at the top, as in Figure 2—figure supplement 1; (3) A view down at the subunit interface of the 40S subunit; (4) A close-up view of the decoding center (A site) and the P site, as in Figure 2g. Each scene is shown twice.	FIG
34	39	C1274	residue_name_number	In scenes 1, 2 and 3, nucleotides C1274, U1191 of the 40S head and G904 of the 40S platform are shown in black to denote the A, P and E sites, respectively.	FIG
41	46	U1191	residue_name_number	In scenes 1, 2 and 3, nucleotides C1274, U1191 of the 40S head and G904 of the 40S platform are shown in black to denote the A, P and E sites, respectively.	FIG
54	57	40S	complex_assembly	In scenes 1, 2 and 3, nucleotides C1274, U1191 of the 40S head and G904 of the 40S platform are shown in black to denote the A, P and E sites, respectively.	FIG
58	62	head	structure_element	In scenes 1, 2 and 3, nucleotides C1274, U1191 of the 40S head and G904 of the 40S platform are shown in black to denote the A, P and E sites, respectively.	FIG
67	71	G904	residue_name_number	In scenes 1, 2 and 3, nucleotides C1274, U1191 of the 40S head and G904 of the 40S platform are shown in black to denote the A, P and E sites, respectively.	FIG
79	91	40S platform	site	In scenes 1, 2 and 3, nucleotides C1274, U1191 of the 40S head and G904 of the 40S platform are shown in black to denote the A, P and E sites, respectively.	FIG
125	141	A, P and E sites	site	In scenes 1, 2 and 3, nucleotides C1274, U1191 of the 40S head and G904 of the 40S platform are shown in black to denote the A, P and E sites, respectively.	FIG
12	17	C1274	residue_name_number	In scene 4, C1274 and U1191 are labeled and shown in yellow; G577, A1755 and A1756 of the 40S body A site and C1637 of the body P site are labeled and shown in orange.	FIG
22	27	U1191	residue_name_number	In scene 4, C1274 and U1191 are labeled and shown in yellow; G577, A1755 and A1756 of the 40S body A site and C1637 of the body P site are labeled and shown in orange.	FIG
61	65	G577	residue_name_number	In scene 4, C1274 and U1191 are labeled and shown in yellow; G577, A1755 and A1756 of the 40S body A site and C1637 of the body P site are labeled and shown in orange.	FIG
67	72	A1755	residue_name_number	In scene 4, C1274 and U1191 are labeled and shown in yellow; G577, A1755 and A1756 of the 40S body A site and C1637 of the body P site are labeled and shown in orange.	FIG
77	82	A1756	residue_name_number	In scene 4, C1274 and U1191 are labeled and shown in yellow; G577, A1755 and A1756 of the 40S body A site and C1637 of the body P site are labeled and shown in orange.	FIG
90	93	40S	complex_assembly	In scene 4, C1274 and U1191 are labeled and shown in yellow; G577, A1755 and A1756 of the 40S body A site and C1637 of the body P site are labeled and shown in orange.	FIG
94	98	body	structure_element	In scene 4, C1274 and U1191 are labeled and shown in yellow; G577, A1755 and A1756 of the 40S body A site and C1637 of the body P site are labeled and shown in orange.	FIG
99	105	A site	site	In scene 4, C1274 and U1191 are labeled and shown in yellow; G577, A1755 and A1756 of the 40S body A site and C1637 of the body P site are labeled and shown in orange.	FIG
110	115	C1637	residue_name_number	In scene 4, C1274 and U1191 are labeled and shown in yellow; G577, A1755 and A1756 of the 40S body A site and C1637 of the body P site are labeled and shown in orange.	FIG
123	127	body	structure_element	In scene 4, C1274 and U1191 are labeled and shown in yellow; G577, A1755 and A1756 of the 40S body A site and C1637 of the body P site are labeled and shown in orange.	FIG
128	134	P site	site	In scene 4, C1274 and U1191 are labeled and shown in yellow; G577, A1755 and A1756 of the 40S body A site and C1637 of the body P site are labeled and shown in orange.	FIG
34	44	structures	evidence	In this work we have captured the structures of the TSV IRES, whose PKI samples positions between the A and P sites (Structures I–IV), as well as in the P site (Structure V).	DISCUSS
52	55	TSV	species	In this work we have captured the structures of the TSV IRES, whose PKI samples positions between the A and P sites (Structures I–IV), as well as in the P site (Structure V).	DISCUSS
56	60	IRES	site	In this work we have captured the structures of the TSV IRES, whose PKI samples positions between the A and P sites (Structures I–IV), as well as in the P site (Structure V).	DISCUSS
68	71	PKI	structure_element	In this work we have captured the structures of the TSV IRES, whose PKI samples positions between the A and P sites (Structures I–IV), as well as in the P site (Structure V).	DISCUSS
102	115	A and P sites	site	In this work we have captured the structures of the TSV IRES, whose PKI samples positions between the A and P sites (Structures I–IV), as well as in the P site (Structure V).	DISCUSS
117	132	Structures I–IV	evidence	In this work we have captured the structures of the TSV IRES, whose PKI samples positions between the A and P sites (Structures I–IV), as well as in the P site (Structure V).	DISCUSS
153	159	P site	site	In this work we have captured the structures of the TSV IRES, whose PKI samples positions between the A and P sites (Structures I–IV), as well as in the P site (Structure V).	DISCUSS
161	172	Structure V	evidence	In this work we have captured the structures of the TSV IRES, whose PKI samples positions between the A and P sites (Structures I–IV), as well as in the P site (Structure V).	DISCUSS
54	64	initiation	protein_state	We propose that together with the previously reported initiation state, these structures represent the trajectory of eEF2-induced IRES translocation (shown as an animation in http://labs.umassmed.edu/korostelevlab/msc/iresmovie.gif and Video 1).	DISCUSS
78	88	structures	evidence	We propose that together with the previously reported initiation state, these structures represent the trajectory of eEF2-induced IRES translocation (shown as an animation in http://labs.umassmed.edu/korostelevlab/msc/iresmovie.gif and Video 1).	DISCUSS
117	121	eEF2	protein	We propose that together with the previously reported initiation state, these structures represent the trajectory of eEF2-induced IRES translocation (shown as an animation in http://labs.umassmed.edu/korostelevlab/msc/iresmovie.gif and Video 1).	DISCUSS
130	134	IRES	site	We propose that together with the previously reported initiation state, these structures represent the trajectory of eEF2-induced IRES translocation (shown as an animation in http://labs.umassmed.edu/korostelevlab/msc/iresmovie.gif and Video 1).	DISCUSS
4	14	structures	evidence	Our structures reveal previously unseen intermediate states of eEF2 or EF-G engagement with the A site, providing the structural basis for the mechanism of translocase action.	DISCUSS
63	67	eEF2	protein	Our structures reveal previously unseen intermediate states of eEF2 or EF-G engagement with the A site, providing the structural basis for the mechanism of translocase action.	DISCUSS
71	75	EF-G	protein	Our structures reveal previously unseen intermediate states of eEF2 or EF-G engagement with the A site, providing the structural basis for the mechanism of translocase action.	DISCUSS
96	102	A site	site	Our structures reveal previously unseen intermediate states of eEF2 or EF-G engagement with the A site, providing the structural basis for the mechanism of translocase action.	DISCUSS
156	167	translocase	protein_type	Our structures reveal previously unseen intermediate states of eEF2 or EF-G engagement with the A site, providing the structural basis for the mechanism of translocase action.	DISCUSS
56	64	eEF2•GTP	complex_assembly	Furthermore, they provide insight into the mechanism of eEF2•GTP association with the pre-translocation ribosome and eEF2•GDP dissociation from the post-translocation ribosome, also delineating the mechanism of translation inhibition by the antifungal drug sordarin.	DISCUSS
86	103	pre-translocation	protein_state	Furthermore, they provide insight into the mechanism of eEF2•GTP association with the pre-translocation ribosome and eEF2•GDP dissociation from the post-translocation ribosome, also delineating the mechanism of translation inhibition by the antifungal drug sordarin.	DISCUSS
104	112	ribosome	complex_assembly	Furthermore, they provide insight into the mechanism of eEF2•GTP association with the pre-translocation ribosome and eEF2•GDP dissociation from the post-translocation ribosome, also delineating the mechanism of translation inhibition by the antifungal drug sordarin.	DISCUSS
117	125	eEF2•GDP	complex_assembly	Furthermore, they provide insight into the mechanism of eEF2•GTP association with the pre-translocation ribosome and eEF2•GDP dissociation from the post-translocation ribosome, also delineating the mechanism of translation inhibition by the antifungal drug sordarin.	DISCUSS
148	166	post-translocation	protein_state	Furthermore, they provide insight into the mechanism of eEF2•GTP association with the pre-translocation ribosome and eEF2•GDP dissociation from the post-translocation ribosome, also delineating the mechanism of translation inhibition by the antifungal drug sordarin.	DISCUSS
167	175	ribosome	complex_assembly	Furthermore, they provide insight into the mechanism of eEF2•GTP association with the pre-translocation ribosome and eEF2•GDP dissociation from the post-translocation ribosome, also delineating the mechanism of translation inhibition by the antifungal drug sordarin.	DISCUSS
257	265	sordarin	chemical	Furthermore, they provide insight into the mechanism of eEF2•GTP association with the pre-translocation ribosome and eEF2•GDP dissociation from the post-translocation ribosome, also delineating the mechanism of translation inhibition by the antifungal drug sordarin.	DISCUSS
37	47	structures	evidence	In summary, the reported ensemble of structures substantially enhances our understanding of the translocation mechanism, including that of tRNAs as discussed below.	DISCUSS
139	144	tRNAs	chemical	In summary, the reported ensemble of structures substantially enhances our understanding of the translocation mechanism, including that of tRNAs as discussed below.	DISCUSS
21	24	TSV	species	Translocation of the TSV IRES on the 40S subunit globally resembles a step of an inchworm (Figure 4; see also Figure 3—figure supplement 2).	DISCUSS
25	29	IRES	site	Translocation of the TSV IRES on the 40S subunit globally resembles a step of an inchworm (Figure 4; see also Figure 3—figure supplement 2).	DISCUSS
37	40	40S	complex_assembly	Translocation of the TSV IRES on the 40S subunit globally resembles a step of an inchworm (Figure 4; see also Figure 3—figure supplement 2).	DISCUSS
41	48	subunit	structure_element	Translocation of the TSV IRES on the 40S subunit globally resembles a step of an inchworm (Figure 4; see also Figure 3—figure supplement 2).	DISCUSS
81	89	inchworm	protein_state	Translocation of the TSV IRES on the 40S subunit globally resembles a step of an inchworm (Figure 4; see also Figure 3—figure supplement 2).	DISCUSS
14	24	initiation	protein_state	At the start (initiation state), the IRES adopts an extended conformation (extended inchworm).	DISCUSS
37	41	IRES	site	At the start (initiation state), the IRES adopts an extended conformation (extended inchworm).	DISCUSS
52	60	extended	protein_state	At the start (initiation state), the IRES adopts an extended conformation (extended inchworm).	DISCUSS
75	92	extended inchworm	protein_state	At the start (initiation state), the IRES adopts an extended conformation (extended inchworm).	DISCUSS
4	15	front 'legs	structure_element	The front 'legs' (SL4 and SL5) of the 5’-domain (front end) are attached to the 40S head proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2).	DISCUSS
18	21	SL4	structure_element	The front 'legs' (SL4 and SL5) of the 5’-domain (front end) are attached to the 40S head proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2).	DISCUSS
26	29	SL5	structure_element	The front 'legs' (SL4 and SL5) of the 5’-domain (front end) are attached to the 40S head proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2).	DISCUSS
38	47	5’-domain	structure_element	The front 'legs' (SL4 and SL5) of the 5’-domain (front end) are attached to the 40S head proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2).	DISCUSS
49	58	front end	structure_element	The front 'legs' (SL4 and SL5) of the 5’-domain (front end) are attached to the 40S head proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2).	DISCUSS
80	83	40S	complex_assembly	The front 'legs' (SL4 and SL5) of the 5’-domain (front end) are attached to the 40S head proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2).	DISCUSS
84	88	head	structure_element	The front 'legs' (SL4 and SL5) of the 5’-domain (front end) are attached to the 40S head proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2).	DISCUSS
98	101	uS7	protein	The front 'legs' (SL4 and SL5) of the 5’-domain (front end) are attached to the 40S head proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2).	DISCUSS
103	107	uS11	protein	The front 'legs' (SL4 and SL5) of the 5’-domain (front end) are attached to the 40S head proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2).	DISCUSS
112	116	eS25	protein	The front 'legs' (SL4 and SL5) of the 5’-domain (front end) are attached to the 40S head proteins uS7, uS11 and eS25 (Figure 3—figure supplement 2).	DISCUSS
0	3	PKI	structure_element	PKI, representing the hind end, is bound in the A site.	DISCUSS
22	30	hind end	structure_element	PKI, representing the hind end, is bound in the A site.	DISCUSS
35	43	bound in	protein_state	PKI, representing the hind end, is bound in the A site.	DISCUSS
48	54	A site	site	PKI, representing the hind end, is bound in the A site.	DISCUSS
23	41	Structures I to IV	evidence	In the first sub-step (Structures I to IV), the hind end advances from the A to the P site and approaches the front end, which remains attached to the 40S surface.	DISCUSS
48	56	hind end	structure_element	In the first sub-step (Structures I to IV), the hind end advances from the A to the P site and approaches the front end, which remains attached to the 40S surface.	DISCUSS
75	90	A to the P site	site	In the first sub-step (Structures I to IV), the hind end advances from the A to the P site and approaches the front end, which remains attached to the 40S surface.	DISCUSS
110	119	front end	structure_element	In the first sub-step (Structures I to IV), the hind end advances from the A to the P site and approaches the front end, which remains attached to the 40S surface.	DISCUSS
151	154	40S	complex_assembly	In the first sub-step (Structures I to IV), the hind end advances from the A to the P site and approaches the front end, which remains attached to the 40S surface.	DISCUSS
35	38	PKI	structure_element	This shortens the distance between PKI and SL4 by up to 20 Å relative to the initiating IRES structure, resulting in a bent IRES conformation (bent inchworm).	DISCUSS
43	46	SL4	structure_element	This shortens the distance between PKI and SL4 by up to 20 Å relative to the initiating IRES structure, resulting in a bent IRES conformation (bent inchworm).	DISCUSS
88	92	IRES	site	This shortens the distance between PKI and SL4 by up to 20 Å relative to the initiating IRES structure, resulting in a bent IRES conformation (bent inchworm).	DISCUSS
93	102	structure	evidence	This shortens the distance between PKI and SL4 by up to 20 Å relative to the initiating IRES structure, resulting in a bent IRES conformation (bent inchworm).	DISCUSS
119	123	bent	protein_state	This shortens the distance between PKI and SL4 by up to 20 Å relative to the initiating IRES structure, resulting in a bent IRES conformation (bent inchworm).	DISCUSS
124	128	IRES	site	This shortens the distance between PKI and SL4 by up to 20 Å relative to the initiating IRES structure, resulting in a bent IRES conformation (bent inchworm).	DISCUSS
143	156	bent inchworm	protein_state	This shortens the distance between PKI and SL4 by up to 20 Å relative to the initiating IRES structure, resulting in a bent IRES conformation (bent inchworm).	DISCUSS
9	27	Structures IV to V	evidence	Finally (Structures IV to V), as the hind end is accommodated in the P site, the front 'legs' advance by departing from their initial binding sites.	DISCUSS
37	45	hind end	structure_element	Finally (Structures IV to V), as the hind end is accommodated in the P site, the front 'legs' advance by departing from their initial binding sites.	DISCUSS
69	75	P site	site	Finally (Structures IV to V), as the hind end is accommodated in the P site, the front 'legs' advance by departing from their initial binding sites.	DISCUSS
81	93	front 'legs'	structure_element	Finally (Structures IV to V), as the hind end is accommodated in the P site, the front 'legs' advance by departing from their initial binding sites.	DISCUSS
126	147	initial binding sites	site	Finally (Structures IV to V), as the hind end is accommodated in the P site, the front 'legs' advance by departing from their initial binding sites.	DISCUSS
18	22	IRES	site	This converts the IRES into an extended conformation, rendering the inchworm prepared for the next translocation step.	DISCUSS
31	39	extended	protein_state	This converts the IRES into an extended conformation, rendering the inchworm prepared for the next translocation step.	DISCUSS
68	76	inchworm	protein_state	This converts the IRES into an extended conformation, rendering the inchworm prepared for the next translocation step.	DISCUSS
27	31	head	structure_element	Notably, at all steps, the head of the IRES inchworm (L1.1 region) is supported by the mobile L1 stalk.	DISCUSS
39	43	IRES	site	Notably, at all steps, the head of the IRES inchworm (L1.1 region) is supported by the mobile L1 stalk.	DISCUSS
44	52	inchworm	protein_state	Notably, at all steps, the head of the IRES inchworm (L1.1 region) is supported by the mobile L1 stalk.	DISCUSS
54	65	L1.1 region	structure_element	Notably, at all steps, the head of the IRES inchworm (L1.1 region) is supported by the mobile L1 stalk.	DISCUSS
87	93	mobile	protein_state	Notably, at all steps, the head of the IRES inchworm (L1.1 region) is supported by the mobile L1 stalk.	DISCUSS
94	102	L1 stalk	structure_element	Notably, at all steps, the head of the IRES inchworm (L1.1 region) is supported by the mobile L1 stalk.	DISCUSS
7	25	post-translocation	protein_state	In the post-translocation CrPV IRES structure, the 5’-domain similarly protrudes between the subunits and interacts with the L1 stalk, as in the initiation state for this IRES.	DISCUSS
26	30	CrPV	species	In the post-translocation CrPV IRES structure, the 5’-domain similarly protrudes between the subunits and interacts with the L1 stalk, as in the initiation state for this IRES.	DISCUSS
31	35	IRES	site	In the post-translocation CrPV IRES structure, the 5’-domain similarly protrudes between the subunits and interacts with the L1 stalk, as in the initiation state for this IRES.	DISCUSS
36	45	structure	evidence	In the post-translocation CrPV IRES structure, the 5’-domain similarly protrudes between the subunits and interacts with the L1 stalk, as in the initiation state for this IRES.	DISCUSS
51	60	5’-domain	structure_element	In the post-translocation CrPV IRES structure, the 5’-domain similarly protrudes between the subunits and interacts with the L1 stalk, as in the initiation state for this IRES.	DISCUSS
125	133	L1 stalk	structure_element	In the post-translocation CrPV IRES structure, the 5’-domain similarly protrudes between the subunits and interacts with the L1 stalk, as in the initiation state for this IRES.	DISCUSS
145	155	initiation	protein_state	In the post-translocation CrPV IRES structure, the 5’-domain similarly protrudes between the subunits and interacts with the L1 stalk, as in the initiation state for this IRES.	DISCUSS
171	175	IRES	site	In the post-translocation CrPV IRES structure, the 5’-domain similarly protrudes between the subunits and interacts with the L1 stalk, as in the initiation state for this IRES.	DISCUSS
46	49	TSV	species	This underlines structural similarity for the TSV and CrPV IRES translocation mechanisms.	DISCUSS
54	58	CrPV	species	This underlines structural similarity for the TSV and CrPV IRES translocation mechanisms.	DISCUSS
59	63	IRES	site	This underlines structural similarity for the TSV and CrPV IRES translocation mechanisms.	DISCUSS
61	67	A site	site	Upon translocation, the GCU start codon is positioned in the A site (Structure V), ready for interaction with Ala-tRNAAla upon eEF2 departure.	DISCUSS
69	80	Structure V	evidence	Upon translocation, the GCU start codon is positioned in the A site (Structure V), ready for interaction with Ala-tRNAAla upon eEF2 departure.	DISCUSS
110	121	Ala-tRNAAla	chemical	Upon translocation, the GCU start codon is positioned in the A site (Structure V), ready for interaction with Ala-tRNAAla upon eEF2 departure.	DISCUSS
127	131	eEF2	protein	Upon translocation, the GCU start codon is positioned in the A site (Structure V), ready for interaction with Ala-tRNAAla upon eEF2 departure.	DISCUSS
59	62	IGR	structure_element	Recent studies have shown that in some cases a fraction of IGR IRES-driven translation results from an alternative reading frame, which is shifted by one nucleotide relative to the normal ORF.	DISCUSS
63	67	IRES	site	Recent studies have shown that in some cases a fraction of IGR IRES-driven translation results from an alternative reading frame, which is shifted by one nucleotide relative to the normal ORF.	DISCUSS
188	191	ORF	structure_element	Recent studies have shown that in some cases a fraction of IGR IRES-driven translation results from an alternative reading frame, which is shifted by one nucleotide relative to the normal ORF.	DISCUSS
78	92	aminoacyl-tRNA	chemical	One of the mechanistic scenarios (discussed in) involves binding of the first aminoacyl-tRNA to the post-translocated IRES mRNA frame shifted by one nucleotide (predominantly a +1 frame shift).	DISCUSS
100	117	post-translocated	protein_state	One of the mechanistic scenarios (discussed in) involves binding of the first aminoacyl-tRNA to the post-translocated IRES mRNA frame shifted by one nucleotide (predominantly a +1 frame shift).	DISCUSS
118	122	IRES	site	One of the mechanistic scenarios (discussed in) involves binding of the first aminoacyl-tRNA to the post-translocated IRES mRNA frame shifted by one nucleotide (predominantly a +1 frame shift).	DISCUSS
123	127	mRNA	chemical	One of the mechanistic scenarios (discussed in) involves binding of the first aminoacyl-tRNA to the post-translocated IRES mRNA frame shifted by one nucleotide (predominantly a +1 frame shift).	DISCUSS
7	17	structures	evidence	In our structures, the IRES presents to the decoding center a pre-translocated or fully translocated ORF, rather than a +1 (more translocated) ORF, suggesting that eEF2 does not induce a highly populated fraction of +1 shifted IRES mRNAs.	DISCUSS
23	27	IRES	site	In our structures, the IRES presents to the decoding center a pre-translocated or fully translocated ORF, rather than a +1 (more translocated) ORF, suggesting that eEF2 does not induce a highly populated fraction of +1 shifted IRES mRNAs.	DISCUSS
44	59	decoding center	site	In our structures, the IRES presents to the decoding center a pre-translocated or fully translocated ORF, rather than a +1 (more translocated) ORF, suggesting that eEF2 does not induce a highly populated fraction of +1 shifted IRES mRNAs.	DISCUSS
62	78	pre-translocated	protein_state	In our structures, the IRES presents to the decoding center a pre-translocated or fully translocated ORF, rather than a +1 (more translocated) ORF, suggesting that eEF2 does not induce a highly populated fraction of +1 shifted IRES mRNAs.	DISCUSS
82	100	fully translocated	protein_state	In our structures, the IRES presents to the decoding center a pre-translocated or fully translocated ORF, rather than a +1 (more translocated) ORF, suggesting that eEF2 does not induce a highly populated fraction of +1 shifted IRES mRNAs.	DISCUSS
101	104	ORF	structure_element	In our structures, the IRES presents to the decoding center a pre-translocated or fully translocated ORF, rather than a +1 (more translocated) ORF, suggesting that eEF2 does not induce a highly populated fraction of +1 shifted IRES mRNAs.	DISCUSS
143	146	ORF	structure_element	In our structures, the IRES presents to the decoding center a pre-translocated or fully translocated ORF, rather than a +1 (more translocated) ORF, suggesting that eEF2 does not induce a highly populated fraction of +1 shifted IRES mRNAs.	DISCUSS
164	168	eEF2	protein	In our structures, the IRES presents to the decoding center a pre-translocated or fully translocated ORF, rather than a +1 (more translocated) ORF, suggesting that eEF2 does not induce a highly populated fraction of +1 shifted IRES mRNAs.	DISCUSS
227	231	IRES	site	In our structures, the IRES presents to the decoding center a pre-translocated or fully translocated ORF, rather than a +1 (more translocated) ORF, suggesting that eEF2 does not induce a highly populated fraction of +1 shifted IRES mRNAs.	DISCUSS
232	237	mRNAs	chemical	In our structures, the IRES presents to the decoding center a pre-translocated or fully translocated ORF, rather than a +1 (more translocated) ORF, suggesting that eEF2 does not induce a highly populated fraction of +1 shifted IRES mRNAs.	DISCUSS
61	65	eEF2	protein	It is likely that alternative frame setting occurs following eEF2 release and that this depends on transient displacement of the start codon in the decoding center, allowing binding of the corresponding amino acyl-tRNA to an off-frame codon.	DISCUSS
148	163	decoding center	site	It is likely that alternative frame setting occurs following eEF2 release and that this depends on transient displacement of the start codon in the decoding center, allowing binding of the corresponding amino acyl-tRNA to an off-frame codon.	DISCUSS
203	218	amino acyl-tRNA	chemical	It is likely that alternative frame setting occurs following eEF2 release and that this depends on transient displacement of the start codon in the decoding center, allowing binding of the corresponding amino acyl-tRNA to an off-frame codon.	DISCUSS
8	26	structural studies	experimental_method	Further structural studies involving 80S•IRES•tRNA complexes are necessary to understand the mechanisms underlying alternative reading frame selection.	DISCUSS
37	50	80S•IRES•tRNA	complex_assembly	Further structural studies involving 80S•IRES•tRNA complexes are necessary to understand the mechanisms underlying alternative reading frame selection.	DISCUSS
4	15	presence of	protein_state	The presence of several translocation complexes in a single sample suggests that the structures represent equilibrium states of forward and reverse translocation of the IRES, which interconvert among each other.	DISCUSS
85	95	structures	evidence	The presence of several translocation complexes in a single sample suggests that the structures represent equilibrium states of forward and reverse translocation of the IRES, which interconvert among each other.	DISCUSS
169	173	IRES	site	The presence of several translocation complexes in a single sample suggests that the structures represent equilibrium states of forward and reverse translocation of the IRES, which interconvert among each other.	DISCUSS
61	66	IRESs	site	This is consistent with the observations that the intergenic IRESs are prone to reverse translocation.	DISCUSS
14	46	biochemical toe-printing studies	experimental_method	Specifically, biochemical toe-printing studies in the presence of eEF2•GTP identified IRES in a non-translocated position unless eEF1a•aa-tRNA is also present.	DISCUSS
54	65	presence of	protein_state	Specifically, biochemical toe-printing studies in the presence of eEF2•GTP identified IRES in a non-translocated position unless eEF1a•aa-tRNA is also present.	DISCUSS
66	74	eEF2•GTP	complex_assembly	Specifically, biochemical toe-printing studies in the presence of eEF2•GTP identified IRES in a non-translocated position unless eEF1a•aa-tRNA is also present.	DISCUSS
86	90	IRES	site	Specifically, biochemical toe-printing studies in the presence of eEF2•GTP identified IRES in a non-translocated position unless eEF1a•aa-tRNA is also present.	DISCUSS
96	112	non-translocated	protein_state	Specifically, biochemical toe-printing studies in the presence of eEF2•GTP identified IRES in a non-translocated position unless eEF1a•aa-tRNA is also present.	DISCUSS
129	142	eEF1a•aa-tRNA	complex_assembly	Specifically, biochemical toe-printing studies in the presence of eEF2•GTP identified IRES in a non-translocated position unless eEF1a•aa-tRNA is also present.	DISCUSS
29	33	IRES	site	These findings indicate that IRES translocation by eEF2 is futile: the IRES returns to the A site upon releasing eEF2•GDP unless an amino-acyl tRNA enters the A site and blocks IRES back-translocation.	DISCUSS
51	55	eEF2	protein	These findings indicate that IRES translocation by eEF2 is futile: the IRES returns to the A site upon releasing eEF2•GDP unless an amino-acyl tRNA enters the A site and blocks IRES back-translocation.	DISCUSS
71	75	IRES	site	These findings indicate that IRES translocation by eEF2 is futile: the IRES returns to the A site upon releasing eEF2•GDP unless an amino-acyl tRNA enters the A site and blocks IRES back-translocation.	DISCUSS
91	97	A site	site	These findings indicate that IRES translocation by eEF2 is futile: the IRES returns to the A site upon releasing eEF2•GDP unless an amino-acyl tRNA enters the A site and blocks IRES back-translocation.	DISCUSS
113	121	eEF2•GDP	complex_assembly	These findings indicate that IRES translocation by eEF2 is futile: the IRES returns to the A site upon releasing eEF2•GDP unless an amino-acyl tRNA enters the A site and blocks IRES back-translocation.	DISCUSS
132	147	amino-acyl tRNA	chemical	These findings indicate that IRES translocation by eEF2 is futile: the IRES returns to the A site upon releasing eEF2•GDP unless an amino-acyl tRNA enters the A site and blocks IRES back-translocation.	DISCUSS
159	165	A site	site	These findings indicate that IRES translocation by eEF2 is futile: the IRES returns to the A site upon releasing eEF2•GDP unless an amino-acyl tRNA enters the A site and blocks IRES back-translocation.	DISCUSS
177	181	IRES	site	These findings indicate that IRES translocation by eEF2 is futile: the IRES returns to the A site upon releasing eEF2•GDP unless an amino-acyl tRNA enters the A site and blocks IRES back-translocation.	DISCUSS
24	41	post-translocated	protein_state	This contrasts with the post-translocated 2tRNA•mRNA complex, in which the classical P and E-site tRNAs are stabilized in the non-rotated ribosome after translocase release.	DISCUSS
42	52	2tRNA•mRNA	complex_assembly	This contrasts with the post-translocated 2tRNA•mRNA complex, in which the classical P and E-site tRNAs are stabilized in the non-rotated ribosome after translocase release.	DISCUSS
85	97	P and E-site	site	This contrasts with the post-translocated 2tRNA•mRNA complex, in which the classical P and E-site tRNAs are stabilized in the non-rotated ribosome after translocase release.	DISCUSS
98	103	tRNAs	chemical	This contrasts with the post-translocated 2tRNA•mRNA complex, in which the classical P and E-site tRNAs are stabilized in the non-rotated ribosome after translocase release.	DISCUSS
126	137	non-rotated	protein_state	This contrasts with the post-translocated 2tRNA•mRNA complex, in which the classical P and E-site tRNAs are stabilized in the non-rotated ribosome after translocase release.	DISCUSS
138	146	ribosome	complex_assembly	This contrasts with the post-translocated 2tRNA•mRNA complex, in which the classical P and E-site tRNAs are stabilized in the non-rotated ribosome after translocase release.	DISCUSS
153	164	translocase	protein_type	This contrasts with the post-translocated 2tRNA•mRNA complex, in which the classical P and E-site tRNAs are stabilized in the non-rotated ribosome after translocase release.	DISCUSS
32	50	post-translocation	protein_state	Thus, the meta-stability of the post-translocation IRES is likely due to the absence of stabilizing structural features present in the 2tRNA•mRNA complex.	DISCUSS
51	55	IRES	site	Thus, the meta-stability of the post-translocation IRES is likely due to the absence of stabilizing structural features present in the 2tRNA•mRNA complex.	DISCUSS
77	87	absence of	protein_state	Thus, the meta-stability of the post-translocation IRES is likely due to the absence of stabilizing structural features present in the 2tRNA•mRNA complex.	DISCUSS
135	145	2tRNA•mRNA	complex_assembly	Thus, the meta-stability of the post-translocation IRES is likely due to the absence of stabilizing structural features present in the 2tRNA•mRNA complex.	DISCUSS
7	17	initiation	protein_state	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
29	33	IRES	site	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
46	63	pre-translocation	protein_state	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
64	74	2tRNA•mRNA	complex_assembly	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
98	101	A/P	site	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
102	106	tRNA	chemical	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
107	126	anticodon-stem loop	structure_element	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
131	136	elbow	structure_element	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
144	150	A site	site	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
159	162	P/E	site	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
163	167	tRNA	chemical	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
168	173	elbow	structure_element	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
189	197	L1 stalk	structure_element	In the initiation state, the IRES resembles a pre-translocation 2tRNA•mRNA complex reduced to the A/P-tRNA anticodon-stem loop and elbow in the A site and the P/E-tRNA elbow contacting the L1 stalk.	DISCUSS
12	31	anticodon-stem loop	structure_element	Because the anticodon-stem loop of the A-tRNA is sufficient for translocation completion, we ascribe the meta-stability of the post-translocation IRES to the absence of the P/E-tRNA elements, either the ASL or the acceptor arm, or both.	DISCUSS
39	40	A	site	Because the anticodon-stem loop of the A-tRNA is sufficient for translocation completion, we ascribe the meta-stability of the post-translocation IRES to the absence of the P/E-tRNA elements, either the ASL or the acceptor arm, or both.	DISCUSS
41	45	tRNA	chemical	Because the anticodon-stem loop of the A-tRNA is sufficient for translocation completion, we ascribe the meta-stability of the post-translocation IRES to the absence of the P/E-tRNA elements, either the ASL or the acceptor arm, or both.	DISCUSS
127	145	post-translocation	protein_state	Because the anticodon-stem loop of the A-tRNA is sufficient for translocation completion, we ascribe the meta-stability of the post-translocation IRES to the absence of the P/E-tRNA elements, either the ASL or the acceptor arm, or both.	DISCUSS
146	150	IRES	site	Because the anticodon-stem loop of the A-tRNA is sufficient for translocation completion, we ascribe the meta-stability of the post-translocation IRES to the absence of the P/E-tRNA elements, either the ASL or the acceptor arm, or both.	DISCUSS
158	168	absence of	protein_state	Because the anticodon-stem loop of the A-tRNA is sufficient for translocation completion, we ascribe the meta-stability of the post-translocation IRES to the absence of the P/E-tRNA elements, either the ASL or the acceptor arm, or both.	DISCUSS
173	176	P/E	site	Because the anticodon-stem loop of the A-tRNA is sufficient for translocation completion, we ascribe the meta-stability of the post-translocation IRES to the absence of the P/E-tRNA elements, either the ASL or the acceptor arm, or both.	DISCUSS
177	181	tRNA	chemical	Because the anticodon-stem loop of the A-tRNA is sufficient for translocation completion, we ascribe the meta-stability of the post-translocation IRES to the absence of the P/E-tRNA elements, either the ASL or the acceptor arm, or both.	DISCUSS
203	206	ASL	structure_element	Because the anticodon-stem loop of the A-tRNA is sufficient for translocation completion, we ascribe the meta-stability of the post-translocation IRES to the absence of the P/E-tRNA elements, either the ASL or the acceptor arm, or both.	DISCUSS
29	32	SL4	structure_element	Furthermore, interactions of SL4 and SL5 with the 40S subunit likely contribute to stabilization of pre-translocation structures.	DISCUSS
37	40	SL5	structure_element	Furthermore, interactions of SL4 and SL5 with the 40S subunit likely contribute to stabilization of pre-translocation structures.	DISCUSS
50	53	40S	complex_assembly	Furthermore, interactions of SL4 and SL5 with the 40S subunit likely contribute to stabilization of pre-translocation structures.	DISCUSS
54	61	subunit	structure_element	Furthermore, interactions of SL4 and SL5 with the 40S subunit likely contribute to stabilization of pre-translocation structures.	DISCUSS
100	117	pre-translocation	protein_state	Furthermore, interactions of SL4 and SL5 with the 40S subunit likely contribute to stabilization of pre-translocation structures.	DISCUSS
118	128	structures	evidence	Furthermore, interactions of SL4 and SL5 with the 40S subunit likely contribute to stabilization of pre-translocation structures.	DISCUSS
21	24	40S	complex_assembly	Partitioned roles of 40S subunit rearrangements	DISCUSS
25	32	subunit	structure_element	Partitioned roles of 40S subunit rearrangements	DISCUSS
4	14	structures	evidence	Our structures delineate the mechanistic functions for intersubunit rotation and head swivel in translocation.	DISCUSS
81	85	head	structure_element	Our structures delineate the mechanistic functions for intersubunit rotation and head swivel in translocation.	DISCUSS
43	47	eEF2	protein	Specifically, intersubunit rotation allows eEF2 entry into the A site, while the head swivel mediates PKI translocation.	DISCUSS
63	69	A site	site	Specifically, intersubunit rotation allows eEF2 entry into the A site, while the head swivel mediates PKI translocation.	DISCUSS
81	85	head	structure_element	Specifically, intersubunit rotation allows eEF2 entry into the A site, while the head swivel mediates PKI translocation.	DISCUSS
102	105	PKI	structure_element	Specifically, intersubunit rotation allows eEF2 entry into the A site, while the head swivel mediates PKI translocation.	DISCUSS
63	78	cryo-EM studies	experimental_method	Various degrees of intersubunit rotation have been observed in cryo-EM studies of the 80S•IRES initiation complexes.	DISCUSS
86	94	80S•IRES	complex_assembly	Various degrees of intersubunit rotation have been observed in cryo-EM studies of the 80S•IRES initiation complexes.	DISCUSS
95	105	initiation	protein_state	Various degrees of intersubunit rotation have been observed in cryo-EM studies of the 80S•IRES initiation complexes.	DISCUSS
23	31	subunits	structure_element	This suggests that the subunits are capable of spontaneous rotation, as is the case for tRNA-bound pre-translocation complexes.	DISCUSS
88	98	tRNA-bound	protein_state	This suggests that the subunits are capable of spontaneous rotation, as is the case for tRNA-bound pre-translocation complexes.	DISCUSS
99	116	pre-translocation	protein_state	This suggests that the subunits are capable of spontaneous rotation, as is the case for tRNA-bound pre-translocation complexes.	DISCUSS
4	21	pre-translocation	protein_state	The pre-translocation Structure I with eEF2 least advanced into the A site adopts a fully rotated conformation.	DISCUSS
22	33	Structure I	evidence	The pre-translocation Structure I with eEF2 least advanced into the A site adopts a fully rotated conformation.	DISCUSS
39	43	eEF2	protein	The pre-translocation Structure I with eEF2 least advanced into the A site adopts a fully rotated conformation.	DISCUSS
68	74	A site	site	The pre-translocation Structure I with eEF2 least advanced into the A site adopts a fully rotated conformation.	DISCUSS
84	110	fully rotated conformation	protein_state	The pre-translocation Structure I with eEF2 least advanced into the A site adopts a fully rotated conformation.	DISCUSS
35	51	Structure I to V	evidence	Reverse intersubunit rotation from Structure I to V shifts the translocation tunnel (the tunnel between the A, P and E sites) toward eEF2, which is rigidly attached to the 60S subunit.	DISCUSS
63	83	translocation tunnel	site	Reverse intersubunit rotation from Structure I to V shifts the translocation tunnel (the tunnel between the A, P and E sites) toward eEF2, which is rigidly attached to the 60S subunit.	DISCUSS
89	95	tunnel	site	Reverse intersubunit rotation from Structure I to V shifts the translocation tunnel (the tunnel between the A, P and E sites) toward eEF2, which is rigidly attached to the 60S subunit.	DISCUSS
108	124	A, P and E sites	site	Reverse intersubunit rotation from Structure I to V shifts the translocation tunnel (the tunnel between the A, P and E sites) toward eEF2, which is rigidly attached to the 60S subunit.	DISCUSS
133	137	eEF2	protein	Reverse intersubunit rotation from Structure I to V shifts the translocation tunnel (the tunnel between the A, P and E sites) toward eEF2, which is rigidly attached to the 60S subunit.	DISCUSS
172	175	60S	complex_assembly	Reverse intersubunit rotation from Structure I to V shifts the translocation tunnel (the tunnel between the A, P and E sites) toward eEF2, which is rigidly attached to the 60S subunit.	DISCUSS
176	183	subunit	structure_element	Reverse intersubunit rotation from Structure I to V shifts the translocation tunnel (the tunnel between the A, P and E sites) toward eEF2, which is rigidly attached to the 60S subunit.	DISCUSS
12	16	eEF2	protein	This allows eEF2 to move into the A site.	DISCUSS
34	40	A site	site	This allows eEF2 to move into the A site.	DISCUSS
67	71	eEF2	protein	As such, reverse intersubunit rotation facilitates full docking of eEF2 in the A site.	DISCUSS
79	85	A site	site	As such, reverse intersubunit rotation facilitates full docking of eEF2 in the A site.	DISCUSS
12	37	histidine-diphthamide tip	site	Because the histidine-diphthamide tip of eEF2 (H583, H694 and Diph699) attaches to the codon-anticodon-like helix of PKI, eEF2 appears to directly force PKI out of the A site.	DISCUSS
41	45	eEF2	protein	Because the histidine-diphthamide tip of eEF2 (H583, H694 and Diph699) attaches to the codon-anticodon-like helix of PKI, eEF2 appears to directly force PKI out of the A site.	DISCUSS
47	51	H583	residue_name_number	Because the histidine-diphthamide tip of eEF2 (H583, H694 and Diph699) attaches to the codon-anticodon-like helix of PKI, eEF2 appears to directly force PKI out of the A site.	DISCUSS
53	57	H694	residue_name_number	Because the histidine-diphthamide tip of eEF2 (H583, H694 and Diph699) attaches to the codon-anticodon-like helix of PKI, eEF2 appears to directly force PKI out of the A site.	DISCUSS
62	69	Diph699	ptm	Because the histidine-diphthamide tip of eEF2 (H583, H694 and Diph699) attaches to the codon-anticodon-like helix of PKI, eEF2 appears to directly force PKI out of the A site.	DISCUSS
87	113	codon-anticodon-like helix	structure_element	Because the histidine-diphthamide tip of eEF2 (H583, H694 and Diph699) attaches to the codon-anticodon-like helix of PKI, eEF2 appears to directly force PKI out of the A site.	DISCUSS
117	120	PKI	structure_element	Because the histidine-diphthamide tip of eEF2 (H583, H694 and Diph699) attaches to the codon-anticodon-like helix of PKI, eEF2 appears to directly force PKI out of the A site.	DISCUSS
122	126	eEF2	protein	Because the histidine-diphthamide tip of eEF2 (H583, H694 and Diph699) attaches to the codon-anticodon-like helix of PKI, eEF2 appears to directly force PKI out of the A site.	DISCUSS
153	156	PKI	structure_element	Because the histidine-diphthamide tip of eEF2 (H583, H694 and Diph699) attaches to the codon-anticodon-like helix of PKI, eEF2 appears to directly force PKI out of the A site.	DISCUSS
168	174	A site	site	Because the histidine-diphthamide tip of eEF2 (H583, H694 and Diph699) attaches to the codon-anticodon-like helix of PKI, eEF2 appears to directly force PKI out of the A site.	DISCUSS
4	8	head	structure_element	The head swivel allows gradual translocation of PKI to the P site, first with respect to the body and then to the head.	DISCUSS
48	51	PKI	structure_element	The head swivel allows gradual translocation of PKI to the P site, first with respect to the body and then to the head.	DISCUSS
59	65	P site	site	The head swivel allows gradual translocation of PKI to the P site, first with respect to the body and then to the head.	DISCUSS
93	97	body	structure_element	The head swivel allows gradual translocation of PKI to the P site, first with respect to the body and then to the head.	DISCUSS
114	118	head	structure_element	The head swivel allows gradual translocation of PKI to the P site, first with respect to the body and then to the head.	DISCUSS
4	18	fully swiveled	protein_state	The fully swiveled conformations of Structures II and III represent the mid-point of translocation, in which PKI relocates between the head A site and body P site.	DISCUSS
36	57	Structures II and III	evidence	The fully swiveled conformations of Structures II and III represent the mid-point of translocation, in which PKI relocates between the head A site and body P site.	DISCUSS
109	112	PKI	structure_element	The fully swiveled conformations of Structures II and III represent the mid-point of translocation, in which PKI relocates between the head A site and body P site.	DISCUSS
135	139	head	structure_element	The fully swiveled conformations of Structures II and III represent the mid-point of translocation, in which PKI relocates between the head A site and body P site.	DISCUSS
140	146	A site	site	The fully swiveled conformations of Structures II and III represent the mid-point of translocation, in which PKI relocates between the head A site and body P site.	DISCUSS
151	155	body	structure_element	The fully swiveled conformations of Structures II and III represent the mid-point of translocation, in which PKI relocates between the head A site and body P site.	DISCUSS
156	162	P site	site	The fully swiveled conformations of Structures II and III represent the mid-point of translocation, in which PKI relocates between the head A site and body P site.	DISCUSS
56	66	2tRNA•mRNA	complex_assembly	We note that such mid-states have not been observed for 2tRNA•mRNA, but their formation can explain the formation of subsequent pe/E hybrid and ap/P chimeric structures (Figure 1—figure supplement 1).	DISCUSS
128	139	pe/E hybrid	protein_state	We note that such mid-states have not been observed for 2tRNA•mRNA, but their formation can explain the formation of subsequent pe/E hybrid and ap/P chimeric structures (Figure 1—figure supplement 1).	DISCUSS
144	157	ap/P chimeric	protein_state	We note that such mid-states have not been observed for 2tRNA•mRNA, but their formation can explain the formation of subsequent pe/E hybrid and ap/P chimeric structures (Figure 1—figure supplement 1).	DISCUSS
158	168	structures	evidence	We note that such mid-states have not been observed for 2tRNA•mRNA, but their formation can explain the formation of subsequent pe/E hybrid and ap/P chimeric structures (Figure 1—figure supplement 1).	DISCUSS
20	38	Structure III to V	evidence	Reverse swivel from Structure III to V brings the head to the non-swiveled position, restoring the A and P sites on the small subunit.	DISCUSS
50	54	head	structure_element	Reverse swivel from Structure III to V brings the head to the non-swiveled position, restoring the A and P sites on the small subunit.	DISCUSS
62	74	non-swiveled	protein_state	Reverse swivel from Structure III to V brings the head to the non-swiveled position, restoring the A and P sites on the small subunit.	DISCUSS
99	112	A and P sites	site	Reverse swivel from Structure III to V brings the head to the non-swiveled position, restoring the A and P sites on the small subunit.	DISCUSS
120	133	small subunit	structure_element	Reverse swivel from Structure III to V brings the head to the non-swiveled position, restoring the A and P sites on the small subunit.	DISCUSS
17	21	eEF2	protein	The functions of eEF2 in translocation	DISCUSS
88	109	ribosomal translocase	protein_type	To our knowledge, our work provides the first high-resolution view of the dynamics of a ribosomal translocase that is inferred from an ensemble of structures sampled under uniform conditions.	DISCUSS
147	157	structures	evidence	To our knowledge, our work provides the first high-resolution view of the dynamics of a ribosomal translocase that is inferred from an ensemble of structures sampled under uniform conditions.	DISCUSS
4	14	structures	evidence	The structures, therefore, offer a unique opportunity to address the role of the elongation factors during translocation.	DISCUSS
81	99	elongation factors	protein_type	The structures, therefore, offer a unique opportunity to address the role of the elongation factors during translocation.	DISCUSS
0	12	Translocases	protein_type	Translocases are efficient enzymes.	DISCUSS
10	18	ribosome	complex_assembly	While the ribosome itself has the capacity to translocate in the absence of the translocase, spontaneous translocation is slow.	DISCUSS
65	75	absence of	protein_state	While the ribosome itself has the capacity to translocate in the absence of the translocase, spontaneous translocation is slow.	DISCUSS
80	91	translocase	protein_type	While the ribosome itself has the capacity to translocate in the absence of the translocase, spontaneous translocation is slow.	DISCUSS
0	4	EF-G	protein	EF-G enhances the translocation rate by several orders of magnitude, aided by an additional 2- to 50-fold boost from GTP hydrolysis.	DISCUSS
117	120	GTP	chemical	EF-G enhances the translocation rate by several orders of magnitude, aided by an additional 2- to 50-fold boost from GTP hydrolysis.	DISCUSS
19	29	structures	evidence	Due to the lack of structures of translocation intermediates, the mechanistic role of eEF2/EF-G is not fully understood.	DISCUSS
86	90	eEF2	protein	Due to the lack of structures of translocation intermediates, the mechanistic role of eEF2/EF-G is not fully understood.	DISCUSS
91	95	EF-G	protein	Due to the lack of structures of translocation intermediates, the mechanistic role of eEF2/EF-G is not fully understood.	DISCUSS
4	17	80S•IRES•eEF2	complex_assembly	The 80S•IRES•eEF2 structures reported here suggest two main roles for eEF2 in translocation.	DISCUSS
18	28	structures	evidence	The 80S•IRES•eEF2 structures reported here suggest two main roles for eEF2 in translocation.	DISCUSS
70	74	eEF2	protein	The 80S•IRES•eEF2 structures reported here suggest two main roles for eEF2 in translocation.	DISCUSS
56	59	PKI	structure_element	As discussed above, the first role is to directly shift PKI out of the A site upon spontaneous reverse intersubunit rotation.	DISCUSS
71	77	A site	site	As discussed above, the first role is to directly shift PKI out of the A site upon spontaneous reverse intersubunit rotation.	DISCUSS
7	17	structures	evidence	In our structures, the tip of domain IV docks next to PKI, with diphthamide 699 fit into the minor groove of the codon-anticodon-like helix of PKI (Figure 7).	DISCUSS
37	39	IV	structure_element	In our structures, the tip of domain IV docks next to PKI, with diphthamide 699 fit into the minor groove of the codon-anticodon-like helix of PKI (Figure 7).	DISCUSS
54	57	PKI	structure_element	In our structures, the tip of domain IV docks next to PKI, with diphthamide 699 fit into the minor groove of the codon-anticodon-like helix of PKI (Figure 7).	DISCUSS
64	79	diphthamide 699	ptm	In our structures, the tip of domain IV docks next to PKI, with diphthamide 699 fit into the minor groove of the codon-anticodon-like helix of PKI (Figure 7).	DISCUSS
93	105	minor groove	site	In our structures, the tip of domain IV docks next to PKI, with diphthamide 699 fit into the minor groove of the codon-anticodon-like helix of PKI (Figure 7).	DISCUSS
113	139	codon-anticodon-like helix	structure_element	In our structures, the tip of domain IV docks next to PKI, with diphthamide 699 fit into the minor groove of the codon-anticodon-like helix of PKI (Figure 7).	DISCUSS
143	146	PKI	structure_element	In our structures, the tip of domain IV docks next to PKI, with diphthamide 699 fit into the minor groove of the codon-anticodon-like helix of PKI (Figure 7).	DISCUSS
46	50	eEF2	protein	This arrangement rationalizes inactivation of eEF2 by diphtheria toxin, which catalyzes ADP-ribosylation of the diphthamide (reviewed in).	DISCUSS
54	70	diphtheria toxin	protein_type	This arrangement rationalizes inactivation of eEF2 by diphtheria toxin, which catalyzes ADP-ribosylation of the diphthamide (reviewed in).	DISCUSS
88	104	ADP-ribosylation	ptm	This arrangement rationalizes inactivation of eEF2 by diphtheria toxin, which catalyzes ADP-ribosylation of the diphthamide (reviewed in).	DISCUSS
112	123	diphthamide	ptm	This arrangement rationalizes inactivation of eEF2 by diphtheria toxin, which catalyzes ADP-ribosylation of the diphthamide (reviewed in).	DISCUSS
11	26	ADP-ribosylates	ptm	The enzyme ADP-ribosylates the NE2 atom of the imidazole ring, which in our structures interacts with the first two residues of the anticodon-like strand of PKI.	DISCUSS
76	86	structures	evidence	The enzyme ADP-ribosylates the NE2 atom of the imidazole ring, which in our structures interacts with the first two residues of the anticodon-like strand of PKI.	DISCUSS
132	153	anticodon-like strand	structure_element	The enzyme ADP-ribosylates the NE2 atom of the imidazole ring, which in our structures interacts with the first two residues of the anticodon-like strand of PKI.	DISCUSS
157	160	PKI	structure_element	The enzyme ADP-ribosylates the NE2 atom of the imidazole ring, which in our structures interacts with the first two residues of the anticodon-like strand of PKI.	DISCUSS
10	13	ADP	chemical	The bulky ADP-ribosyl moiety at this position would disrupt the interaction, rendering eEF2 unable to bind to the A site and/or stalled on ribosomes in a non-productive conformation.	DISCUSS
87	91	eEF2	protein	The bulky ADP-ribosyl moiety at this position would disrupt the interaction, rendering eEF2 unable to bind to the A site and/or stalled on ribosomes in a non-productive conformation.	DISCUSS
114	120	A site	site	The bulky ADP-ribosyl moiety at this position would disrupt the interaction, rendering eEF2 unable to bind to the A site and/or stalled on ribosomes in a non-productive conformation.	DISCUSS
139	148	ribosomes	complex_assembly	The bulky ADP-ribosyl moiety at this position would disrupt the interaction, rendering eEF2 unable to bind to the A site and/or stalled on ribosomes in a non-productive conformation.	DISCUSS
3	7	eEF2	protein	As eEF2 shifts PKI toward the P site in the course of reverse intersubunit rotation, the 60S-attached translocase migrates along the surface of the 40S subunit, guided by electrostatic interactions.	DISCUSS
15	18	PKI	structure_element	As eEF2 shifts PKI toward the P site in the course of reverse intersubunit rotation, the 60S-attached translocase migrates along the surface of the 40S subunit, guided by electrostatic interactions.	DISCUSS
30	36	P site	site	As eEF2 shifts PKI toward the P site in the course of reverse intersubunit rotation, the 60S-attached translocase migrates along the surface of the 40S subunit, guided by electrostatic interactions.	DISCUSS
89	101	60S-attached	protein_state	As eEF2 shifts PKI toward the P site in the course of reverse intersubunit rotation, the 60S-attached translocase migrates along the surface of the 40S subunit, guided by electrostatic interactions.	DISCUSS
102	113	translocase	protein_type	As eEF2 shifts PKI toward the P site in the course of reverse intersubunit rotation, the 60S-attached translocase migrates along the surface of the 40S subunit, guided by electrostatic interactions.	DISCUSS
148	151	40S	complex_assembly	As eEF2 shifts PKI toward the P site in the course of reverse intersubunit rotation, the 60S-attached translocase migrates along the surface of the 40S subunit, guided by electrostatic interactions.	DISCUSS
152	159	subunit	structure_element	As eEF2 shifts PKI toward the P site in the course of reverse intersubunit rotation, the 60S-attached translocase migrates along the surface of the 40S subunit, guided by electrostatic interactions.	DISCUSS
171	197	electrostatic interactions	bond_interaction	As eEF2 shifts PKI toward the P site in the course of reverse intersubunit rotation, the 60S-attached translocase migrates along the surface of the 40S subunit, guided by electrostatic interactions.	DISCUSS
0	26	Positively-charged patches	site	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
38	40	II	structure_element	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
45	48	III	structure_element	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
50	54	R391	residue_name_number	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
56	60	K394	residue_name_number	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
62	66	R433	residue_name_number	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
68	72	R510	residue_name_number	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
78	80	IV	structure_element	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
82	86	K613	residue_name_number	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
88	92	R617	residue_name_number	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
94	98	R609	residue_name_number	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
100	104	R631	residue_name_number	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
106	110	K651	residue_name_number	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
123	127	rRNA	chemical	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
135	138	40S	complex_assembly	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
139	143	body	structure_element	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
145	147	h5	structure_element	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
153	157	head	structure_element	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
159	162	h18	structure_element	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
167	170	h33	structure_element	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
171	174	h34	structure_element	Positively-charged patches of domains II and III (R391, K394, R433, R510) and IV (K613, R617, R609, R631, K651) slide over rRNA of the 40S body (h5) and head (h18 and h33/h34), respectively.	DISCUSS
4	14	Structures	evidence	The Structures reveal hopping of the positive clusters over rRNA helices.	DISCUSS
60	64	rRNA	chemical	The Structures reveal hopping of the positive clusters over rRNA helices.	DISCUSS
65	72	helices	structure_element	The Structures reveal hopping of the positive clusters over rRNA helices.	DISCUSS
21	40	Structures II and V	evidence	For example, between Structures II and V, the K613/R617/R631 cluster of domain IV hops by ~19 Å (for Cα of R617) from the phosphate backbone of h33 (at nt 1261–1264) to that of the neighboring h34 (at nt 1442–1445).	DISCUSS
46	50	K613	residue_name_number	For example, between Structures II and V, the K613/R617/R631 cluster of domain IV hops by ~19 Å (for Cα of R617) from the phosphate backbone of h33 (at nt 1261–1264) to that of the neighboring h34 (at nt 1442–1445).	DISCUSS
51	55	R617	residue_name_number	For example, between Structures II and V, the K613/R617/R631 cluster of domain IV hops by ~19 Å (for Cα of R617) from the phosphate backbone of h33 (at nt 1261–1264) to that of the neighboring h34 (at nt 1442–1445).	DISCUSS
56	60	R631	residue_name_number	For example, between Structures II and V, the K613/R617/R631 cluster of domain IV hops by ~19 Å (for Cα of R617) from the phosphate backbone of h33 (at nt 1261–1264) to that of the neighboring h34 (at nt 1442–1445).	DISCUSS
79	81	IV	structure_element	For example, between Structures II and V, the K613/R617/R631 cluster of domain IV hops by ~19 Å (for Cα of R617) from the phosphate backbone of h33 (at nt 1261–1264) to that of the neighboring h34 (at nt 1442–1445).	DISCUSS
107	111	R617	residue_name_number	For example, between Structures II and V, the K613/R617/R631 cluster of domain IV hops by ~19 Å (for Cα of R617) from the phosphate backbone of h33 (at nt 1261–1264) to that of the neighboring h34 (at nt 1442–1445).	DISCUSS
144	147	h33	structure_element	For example, between Structures II and V, the K613/R617/R631 cluster of domain IV hops by ~19 Å (for Cα of R617) from the phosphate backbone of h33 (at nt 1261–1264) to that of the neighboring h34 (at nt 1442–1445).	DISCUSS
155	164	1261–1264	residue_range	For example, between Structures II and V, the K613/R617/R631 cluster of domain IV hops by ~19 Å (for Cα of R617) from the phosphate backbone of h33 (at nt 1261–1264) to that of the neighboring h34 (at nt 1442–1445).	DISCUSS
193	196	h34	structure_element	For example, between Structures II and V, the K613/R617/R631 cluster of domain IV hops by ~19 Å (for Cα of R617) from the phosphate backbone of h33 (at nt 1261–1264) to that of the neighboring h34 (at nt 1442–1445).	DISCUSS
204	213	1442–1445	residue_range	For example, between Structures II and V, the K613/R617/R631 cluster of domain IV hops by ~19 Å (for Cα of R617) from the phosphate backbone of h33 (at nt 1261–1264) to that of the neighboring h34 (at nt 1442–1445).	DISCUSS
17	21	eEF2	protein	Thus, sliding of eEF2 involves reorganization of electrostatic, perhaps isoenergetic interactions, echoing those implied in extraordinarily fast ribosome inactivation rates by the small-protein ribotoxins and in fast protein association and diffusion along DNA.	DISCUSS
49	97	electrostatic, perhaps isoenergetic interactions	bond_interaction	Thus, sliding of eEF2 involves reorganization of electrostatic, perhaps isoenergetic interactions, echoing those implied in extraordinarily fast ribosome inactivation rates by the small-protein ribotoxins and in fast protein association and diffusion along DNA.	DISCUSS
145	153	ribosome	complex_assembly	Thus, sliding of eEF2 involves reorganization of electrostatic, perhaps isoenergetic interactions, echoing those implied in extraordinarily fast ribosome inactivation rates by the small-protein ribotoxins and in fast protein association and diffusion along DNA.	DISCUSS
0	10	Comparison	experimental_method	Comparison of our structures with the 80S•IRES initiation structure reveals the structural basis for the second key function of the translocase: 'unlocking' of intrasubunit rearrangements that are required for step-wise translocation of PKI on the small subunit.	DISCUSS
18	28	structures	evidence	Comparison of our structures with the 80S•IRES initiation structure reveals the structural basis for the second key function of the translocase: 'unlocking' of intrasubunit rearrangements that are required for step-wise translocation of PKI on the small subunit.	DISCUSS
38	46	80S•IRES	complex_assembly	Comparison of our structures with the 80S•IRES initiation structure reveals the structural basis for the second key function of the translocase: 'unlocking' of intrasubunit rearrangements that are required for step-wise translocation of PKI on the small subunit.	DISCUSS
47	57	initiation	protein_state	Comparison of our structures with the 80S•IRES initiation structure reveals the structural basis for the second key function of the translocase: 'unlocking' of intrasubunit rearrangements that are required for step-wise translocation of PKI on the small subunit.	DISCUSS
58	67	structure	evidence	Comparison of our structures with the 80S•IRES initiation structure reveals the structural basis for the second key function of the translocase: 'unlocking' of intrasubunit rearrangements that are required for step-wise translocation of PKI on the small subunit.	DISCUSS
132	143	translocase	protein_type	Comparison of our structures with the 80S•IRES initiation structure reveals the structural basis for the second key function of the translocase: 'unlocking' of intrasubunit rearrangements that are required for step-wise translocation of PKI on the small subunit.	DISCUSS
237	240	PKI	structure_element	Comparison of our structures with the 80S•IRES initiation structure reveals the structural basis for the second key function of the translocase: 'unlocking' of intrasubunit rearrangements that are required for step-wise translocation of PKI on the small subunit.	DISCUSS
248	261	small subunit	structure_element	Comparison of our structures with the 80S•IRES initiation structure reveals the structural basis for the second key function of the translocase: 'unlocking' of intrasubunit rearrangements that are required for step-wise translocation of PKI on the small subunit.	DISCUSS
27	46	ribosome•2tRNA•mRNA	complex_assembly	The unlocking model of the ribosome•2tRNA•mRNA pre-translocation complex has been proposed decades ago and functional requirement of the translocase in this process has been implicated.	DISCUSS
47	64	pre-translocation	protein_state	The unlocking model of the ribosome•2tRNA•mRNA pre-translocation complex has been proposed decades ago and functional requirement of the translocase in this process has been implicated.	DISCUSS
137	148	translocase	protein_type	The unlocking model of the ribosome•2tRNA•mRNA pre-translocation complex has been proposed decades ago and functional requirement of the translocase in this process has been implicated.	DISCUSS
59	65	locked	protein_state	However, the structural and mechanistic definitions of the locked and unlocked states have remained unclear, ranging from the globally distinct ribosome conformations to unknown local rearrangements, e.g. those in the decoding center.	DISCUSS
70	78	unlocked	protein_state	However, the structural and mechanistic definitions of the locked and unlocked states have remained unclear, ranging from the globally distinct ribosome conformations to unknown local rearrangements, e.g. those in the decoding center.	DISCUSS
144	152	ribosome	complex_assembly	However, the structural and mechanistic definitions of the locked and unlocked states have remained unclear, ranging from the globally distinct ribosome conformations to unknown local rearrangements, e.g. those in the decoding center.	DISCUSS
218	233	decoding center	site	However, the structural and mechanistic definitions of the locked and unlocked states have remained unclear, ranging from the globally distinct ribosome conformations to unknown local rearrangements, e.g. those in the decoding center.	DISCUSS
0	9	FRET data	evidence	FRET data indicate that translocation of 2tRNA•mRNA on the 70S ribosome requires a forward-and-reverse head swivel, which may be related to the unlocking phenomenon.	DISCUSS
41	51	2tRNA•mRNA	complex_assembly	FRET data indicate that translocation of 2tRNA•mRNA on the 70S ribosome requires a forward-and-reverse head swivel, which may be related to the unlocking phenomenon.	DISCUSS
59	71	70S ribosome	complex_assembly	FRET data indicate that translocation of 2tRNA•mRNA on the 70S ribosome requires a forward-and-reverse head swivel, which may be related to the unlocking phenomenon.	DISCUSS
103	107	head	structure_element	FRET data indicate that translocation of 2tRNA•mRNA on the 70S ribosome requires a forward-and-reverse head swivel, which may be related to the unlocking phenomenon.	DISCUSS
37	54	pre-translocation	protein_state	Whereas intersubunit rotation of the pre-translocation complex occurs spontaneously, the head swivel is induced by the eEF2/EF-G translocase, consistent with requirement of eEF2 for unlocking.	DISCUSS
89	93	head	structure_element	Whereas intersubunit rotation of the pre-translocation complex occurs spontaneously, the head swivel is induced by the eEF2/EF-G translocase, consistent with requirement of eEF2 for unlocking.	DISCUSS
119	123	eEF2	protein	Whereas intersubunit rotation of the pre-translocation complex occurs spontaneously, the head swivel is induced by the eEF2/EF-G translocase, consistent with requirement of eEF2 for unlocking.	DISCUSS
124	128	EF-G	protein	Whereas intersubunit rotation of the pre-translocation complex occurs spontaneously, the head swivel is induced by the eEF2/EF-G translocase, consistent with requirement of eEF2 for unlocking.	DISCUSS
129	140	translocase	protein_type	Whereas intersubunit rotation of the pre-translocation complex occurs spontaneously, the head swivel is induced by the eEF2/EF-G translocase, consistent with requirement of eEF2 for unlocking.	DISCUSS
173	177	eEF2	protein	Whereas intersubunit rotation of the pre-translocation complex occurs spontaneously, the head swivel is induced by the eEF2/EF-G translocase, consistent with requirement of eEF2 for unlocking.	DISCUSS
0	18	Structural studies	experimental_method	Structural studies revealed large head swivels in various 70S•tRNA•EF-G and 80S•tRNA•eEF2 complexes, but not in 'locked' complexes with the A site occupied by the tRNA in the absence of the translocase.	DISCUSS
34	38	head	structure_element	Structural studies revealed large head swivels in various 70S•tRNA•EF-G and 80S•tRNA•eEF2 complexes, but not in 'locked' complexes with the A site occupied by the tRNA in the absence of the translocase.	DISCUSS
58	71	70S•tRNA•EF-G	complex_assembly	Structural studies revealed large head swivels in various 70S•tRNA•EF-G and 80S•tRNA•eEF2 complexes, but not in 'locked' complexes with the A site occupied by the tRNA in the absence of the translocase.	DISCUSS
76	89	80S•tRNA•eEF2	complex_assembly	Structural studies revealed large head swivels in various 70S•tRNA•EF-G and 80S•tRNA•eEF2 complexes, but not in 'locked' complexes with the A site occupied by the tRNA in the absence of the translocase.	DISCUSS
113	119	locked	protein_state	Structural studies revealed large head swivels in various 70S•tRNA•EF-G and 80S•tRNA•eEF2 complexes, but not in 'locked' complexes with the A site occupied by the tRNA in the absence of the translocase.	DISCUSS
121	135	complexes with	protein_state	Structural studies revealed large head swivels in various 70S•tRNA•EF-G and 80S•tRNA•eEF2 complexes, but not in 'locked' complexes with the A site occupied by the tRNA in the absence of the translocase.	DISCUSS
140	146	A site	site	Structural studies revealed large head swivels in various 70S•tRNA•EF-G and 80S•tRNA•eEF2 complexes, but not in 'locked' complexes with the A site occupied by the tRNA in the absence of the translocase.	DISCUSS
163	167	tRNA	chemical	Structural studies revealed large head swivels in various 70S•tRNA•EF-G and 80S•tRNA•eEF2 complexes, but not in 'locked' complexes with the A site occupied by the tRNA in the absence of the translocase.	DISCUSS
175	185	absence of	protein_state	Structural studies revealed large head swivels in various 70S•tRNA•EF-G and 80S•tRNA•eEF2 complexes, but not in 'locked' complexes with the A site occupied by the tRNA in the absence of the translocase.	DISCUSS
190	201	translocase	protein_type	Structural studies revealed large head swivels in various 70S•tRNA•EF-G and 80S•tRNA•eEF2 complexes, but not in 'locked' complexes with the A site occupied by the tRNA in the absence of the translocase.	DISCUSS
4	14	structures	evidence	Our structures suggest that eEF2 induces head swivel by 'unlocking' the head-body interactions (Figure 7).	DISCUSS
28	32	eEF2	protein	Our structures suggest that eEF2 induces head swivel by 'unlocking' the head-body interactions (Figure 7).	DISCUSS
41	45	head	structure_element	Our structures suggest that eEF2 induces head swivel by 'unlocking' the head-body interactions (Figure 7).	DISCUSS
72	76	head	structure_element	Our structures suggest that eEF2 induces head swivel by 'unlocking' the head-body interactions (Figure 7).	DISCUSS
77	81	body	structure_element	Our structures suggest that eEF2 induces head swivel by 'unlocking' the head-body interactions (Figure 7).	DISCUSS
15	18	ASL	structure_element	Binding of the ASL to the A site is known from structural studies of bacterial ribosomes to result in 'domain closure' of the small subunit, i.e. closer association of the head, shoulder and body domains.	DISCUSS
26	32	A site	site	Binding of the ASL to the A site is known from structural studies of bacterial ribosomes to result in 'domain closure' of the small subunit, i.e. closer association of the head, shoulder and body domains.	DISCUSS
47	65	structural studies	experimental_method	Binding of the ASL to the A site is known from structural studies of bacterial ribosomes to result in 'domain closure' of the small subunit, i.e. closer association of the head, shoulder and body domains.	DISCUSS
69	78	bacterial	taxonomy_domain	Binding of the ASL to the A site is known from structural studies of bacterial ribosomes to result in 'domain closure' of the small subunit, i.e. closer association of the head, shoulder and body domains.	DISCUSS
79	88	ribosomes	complex_assembly	Binding of the ASL to the A site is known from structural studies of bacterial ribosomes to result in 'domain closure' of the small subunit, i.e. closer association of the head, shoulder and body domains.	DISCUSS
103	117	domain closure	protein_state	Binding of the ASL to the A site is known from structural studies of bacterial ribosomes to result in 'domain closure' of the small subunit, i.e. closer association of the head, shoulder and body domains.	DISCUSS
126	139	small subunit	structure_element	Binding of the ASL to the A site is known from structural studies of bacterial ribosomes to result in 'domain closure' of the small subunit, i.e. closer association of the head, shoulder and body domains.	DISCUSS
172	176	head	structure_element	Binding of the ASL to the A site is known from structural studies of bacterial ribosomes to result in 'domain closure' of the small subunit, i.e. closer association of the head, shoulder and body domains.	DISCUSS
178	186	shoulder	structure_element	Binding of the ASL to the A site is known from structural studies of bacterial ribosomes to result in 'domain closure' of the small subunit, i.e. closer association of the head, shoulder and body domains.	DISCUSS
191	195	body	structure_element	Binding of the ASL to the A site is known from structural studies of bacterial ribosomes to result in 'domain closure' of the small subunit, i.e. closer association of the head, shoulder and body domains.	DISCUSS
35	39	tRNA	chemical	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
47	53	A site	site	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
58	66	stacking	bond_interaction	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
74	78	head	structure_element	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
79	85	A site	site	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
87	92	C1274	residue_name_number	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
96	109	S. cerevisiae	species	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
113	118	C1054	residue_name_number	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
122	129	E. coli	species	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
157	161	body	structure_element	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
162	168	A-site	site	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
181	186	A1755	residue_name_number	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
191	196	A1756	residue_name_number	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
198	203	A1492	residue_name_number	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
208	213	A1493	residue_name_number	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
217	224	E. coli	species	The domain closure 'locks' cognate tRNA in the A site via stacking on the head A site (C1274 in S. cerevisiae or C1054 in E. coli) and interactions with the body A-site nucleotides A1755 and A1756 (A1492 and A1493 in E. coli).	DISCUSS
6	12	locked	protein_state	This 'locked' state is identical to that observed for PKI in the 80S•IRES initiation structures in the absence of eEF2.	DISCUSS
54	57	PKI	structure_element	This 'locked' state is identical to that observed for PKI in the 80S•IRES initiation structures in the absence of eEF2.	DISCUSS
65	73	80S•IRES	complex_assembly	This 'locked' state is identical to that observed for PKI in the 80S•IRES initiation structures in the absence of eEF2.	DISCUSS
74	84	initiation	protein_state	This 'locked' state is identical to that observed for PKI in the 80S•IRES initiation structures in the absence of eEF2.	DISCUSS
85	95	structures	evidence	This 'locked' state is identical to that observed for PKI in the 80S•IRES initiation structures in the absence of eEF2.	DISCUSS
103	113	absence of	protein_state	This 'locked' state is identical to that observed for PKI in the 80S•IRES initiation structures in the absence of eEF2.	DISCUSS
114	118	eEF2	protein	This 'locked' state is identical to that observed for PKI in the 80S•IRES initiation structures in the absence of eEF2.	DISCUSS
0	11	Structure I	evidence	Structure I demonstrates that at an early pre-translocation step, the histidine-diphthamide tip of eEF2 is wedged between A1755 and A1756 and PKI.	DISCUSS
42	59	pre-translocation	protein_state	Structure I demonstrates that at an early pre-translocation step, the histidine-diphthamide tip of eEF2 is wedged between A1755 and A1756 and PKI.	DISCUSS
70	95	histidine-diphthamide tip	site	Structure I demonstrates that at an early pre-translocation step, the histidine-diphthamide tip of eEF2 is wedged between A1755 and A1756 and PKI.	DISCUSS
99	103	eEF2	protein	Structure I demonstrates that at an early pre-translocation step, the histidine-diphthamide tip of eEF2 is wedged between A1755 and A1756 and PKI.	DISCUSS
122	127	A1755	residue_name_number	Structure I demonstrates that at an early pre-translocation step, the histidine-diphthamide tip of eEF2 is wedged between A1755 and A1756 and PKI.	DISCUSS
132	137	A1756	residue_name_number	Structure I demonstrates that at an early pre-translocation step, the histidine-diphthamide tip of eEF2 is wedged between A1755 and A1756 and PKI.	DISCUSS
142	145	PKI	structure_element	Structure I demonstrates that at an early pre-translocation step, the histidine-diphthamide tip of eEF2 is wedged between A1755 and A1756 and PKI.	DISCUSS
28	31	PKI	structure_element	This destabilization allows PKI to detach from the body A site upon spontaneous reverse 40S body rotation, while maintaining interactions with the head A site.	DISCUSS
51	55	body	structure_element	This destabilization allows PKI to detach from the body A site upon spontaneous reverse 40S body rotation, while maintaining interactions with the head A site.	DISCUSS
56	62	A site	site	This destabilization allows PKI to detach from the body A site upon spontaneous reverse 40S body rotation, while maintaining interactions with the head A site.	DISCUSS
88	91	40S	complex_assembly	This destabilization allows PKI to detach from the body A site upon spontaneous reverse 40S body rotation, while maintaining interactions with the head A site.	DISCUSS
92	96	body	structure_element	This destabilization allows PKI to detach from the body A site upon spontaneous reverse 40S body rotation, while maintaining interactions with the head A site.	DISCUSS
147	151	head	structure_element	This destabilization allows PKI to detach from the body A site upon spontaneous reverse 40S body rotation, while maintaining interactions with the head A site.	DISCUSS
152	158	A site	site	This destabilization allows PKI to detach from the body A site upon spontaneous reverse 40S body rotation, while maintaining interactions with the head A site.	DISCUSS
23	33	head-bound	protein_state	Destabilization of the head-bound PKI at the body A site thus allows mobility of the head relative to the body.	DISCUSS
34	37	PKI	structure_element	Destabilization of the head-bound PKI at the body A site thus allows mobility of the head relative to the body.	DISCUSS
45	49	body	structure_element	Destabilization of the head-bound PKI at the body A site thus allows mobility of the head relative to the body.	DISCUSS
50	56	A site	site	Destabilization of the head-bound PKI at the body A site thus allows mobility of the head relative to the body.	DISCUSS
85	89	head	structure_element	Destabilization of the head-bound PKI at the body A site thus allows mobility of the head relative to the body.	DISCUSS
106	110	body	structure_element	Destabilization of the head-bound PKI at the body A site thus allows mobility of the head relative to the body.	DISCUSS
4	25	histidine-diphthamide	ptm	The histidine-diphthamide-induced disengagement of PKI from A1755 and A1756 therefore provides the structural definition for the 'unlocking' mode of eEF2 action.	DISCUSS
51	54	PKI	structure_element	The histidine-diphthamide-induced disengagement of PKI from A1755 and A1756 therefore provides the structural definition for the 'unlocking' mode of eEF2 action.	DISCUSS
60	65	A1755	residue_name_number	The histidine-diphthamide-induced disengagement of PKI from A1755 and A1756 therefore provides the structural definition for the 'unlocking' mode of eEF2 action.	DISCUSS
70	75	A1756	residue_name_number	The histidine-diphthamide-induced disengagement of PKI from A1755 and A1756 therefore provides the structural definition for the 'unlocking' mode of eEF2 action.	DISCUSS
149	153	eEF2	protein	The histidine-diphthamide-induced disengagement of PKI from A1755 and A1756 therefore provides the structural definition for the 'unlocking' mode of eEF2 action.	DISCUSS
16	26	structures	evidence	In summary, our structures are consistent with a model of eEF2-induced translocation in which both PKI and eEF2 passively migrate into the P and A site, respectively, during spontaneous 40S body rotation and head swivel, the latter being allowed by 'unlocking' of the A site by eEF2.	DISCUSS
58	62	eEF2	protein	In summary, our structures are consistent with a model of eEF2-induced translocation in which both PKI and eEF2 passively migrate into the P and A site, respectively, during spontaneous 40S body rotation and head swivel, the latter being allowed by 'unlocking' of the A site by eEF2.	DISCUSS
99	102	PKI	structure_element	In summary, our structures are consistent with a model of eEF2-induced translocation in which both PKI and eEF2 passively migrate into the P and A site, respectively, during spontaneous 40S body rotation and head swivel, the latter being allowed by 'unlocking' of the A site by eEF2.	DISCUSS
107	111	eEF2	protein	In summary, our structures are consistent with a model of eEF2-induced translocation in which both PKI and eEF2 passively migrate into the P and A site, respectively, during spontaneous 40S body rotation and head swivel, the latter being allowed by 'unlocking' of the A site by eEF2.	DISCUSS
139	151	P and A site	site	In summary, our structures are consistent with a model of eEF2-induced translocation in which both PKI and eEF2 passively migrate into the P and A site, respectively, during spontaneous 40S body rotation and head swivel, the latter being allowed by 'unlocking' of the A site by eEF2.	DISCUSS
186	189	40S	complex_assembly	In summary, our structures are consistent with a model of eEF2-induced translocation in which both PKI and eEF2 passively migrate into the P and A site, respectively, during spontaneous 40S body rotation and head swivel, the latter being allowed by 'unlocking' of the A site by eEF2.	DISCUSS
190	194	body	structure_element	In summary, our structures are consistent with a model of eEF2-induced translocation in which both PKI and eEF2 passively migrate into the P and A site, respectively, during spontaneous 40S body rotation and head swivel, the latter being allowed by 'unlocking' of the A site by eEF2.	DISCUSS
208	212	head	structure_element	In summary, our structures are consistent with a model of eEF2-induced translocation in which both PKI and eEF2 passively migrate into the P and A site, respectively, during spontaneous 40S body rotation and head swivel, the latter being allowed by 'unlocking' of the A site by eEF2.	DISCUSS
268	274	A site	site	In summary, our structures are consistent with a model of eEF2-induced translocation in which both PKI and eEF2 passively migrate into the P and A site, respectively, during spontaneous 40S body rotation and head swivel, the latter being allowed by 'unlocking' of the A site by eEF2.	DISCUSS
278	282	eEF2	protein	In summary, our structures are consistent with a model of eEF2-induced translocation in which both PKI and eEF2 passively migrate into the P and A site, respectively, during spontaneous 40S body rotation and head swivel, the latter being allowed by 'unlocking' of the A site by eEF2.	DISCUSS
25	28	PKI	structure_element	Observation of different PKI conformations sampling a range of positions between the A and P sites in the presence of eEF2•GDP implies that thermal fluctuations of the 40S head domain are sufficient for translocation along the energetically flat trajectory.	DISCUSS
85	98	A and P sites	site	Observation of different PKI conformations sampling a range of positions between the A and P sites in the presence of eEF2•GDP implies that thermal fluctuations of the 40S head domain are sufficient for translocation along the energetically flat trajectory.	DISCUSS
106	117	presence of	protein_state	Observation of different PKI conformations sampling a range of positions between the A and P sites in the presence of eEF2•GDP implies that thermal fluctuations of the 40S head domain are sufficient for translocation along the energetically flat trajectory.	DISCUSS
118	126	eEF2•GDP	complex_assembly	Observation of different PKI conformations sampling a range of positions between the A and P sites in the presence of eEF2•GDP implies that thermal fluctuations of the 40S head domain are sufficient for translocation along the energetically flat trajectory.	DISCUSS
168	171	40S	complex_assembly	Observation of different PKI conformations sampling a range of positions between the A and P sites in the presence of eEF2•GDP implies that thermal fluctuations of the 40S head domain are sufficient for translocation along the energetically flat trajectory.	DISCUSS
172	176	head	structure_element	Observation of different PKI conformations sampling a range of positions between the A and P sites in the presence of eEF2•GDP implies that thermal fluctuations of the 40S head domain are sufficient for translocation along the energetically flat trajectory.	DISCUSS
14	18	eEF2	protein	Insights into eEF2 association with and dissociation from the ribosome	DISCUSS
62	70	ribosome	complex_assembly	Insights into eEF2 association with and dissociation from the ribosome	DISCUSS
37	41	eEF2	protein	The conformational rearrangements in eEF2 from Structure I through Structure V provide insights into the mechanisms of eEF2 association with the pre-translocation ribosome and dissociation from the post-translocation ribosome.	DISCUSS
47	58	Structure I	evidence	The conformational rearrangements in eEF2 from Structure I through Structure V provide insights into the mechanisms of eEF2 association with the pre-translocation ribosome and dissociation from the post-translocation ribosome.	DISCUSS
67	78	Structure V	evidence	The conformational rearrangements in eEF2 from Structure I through Structure V provide insights into the mechanisms of eEF2 association with the pre-translocation ribosome and dissociation from the post-translocation ribosome.	DISCUSS
119	123	eEF2	protein	The conformational rearrangements in eEF2 from Structure I through Structure V provide insights into the mechanisms of eEF2 association with the pre-translocation ribosome and dissociation from the post-translocation ribosome.	DISCUSS
145	162	pre-translocation	protein_state	The conformational rearrangements in eEF2 from Structure I through Structure V provide insights into the mechanisms of eEF2 association with the pre-translocation ribosome and dissociation from the post-translocation ribosome.	DISCUSS
163	171	ribosome	complex_assembly	The conformational rearrangements in eEF2 from Structure I through Structure V provide insights into the mechanisms of eEF2 association with the pre-translocation ribosome and dissociation from the post-translocation ribosome.	DISCUSS
198	216	post-translocation	protein_state	The conformational rearrangements in eEF2 from Structure I through Structure V provide insights into the mechanisms of eEF2 association with the pre-translocation ribosome and dissociation from the post-translocation ribosome.	DISCUSS
217	225	ribosome	complex_assembly	The conformational rearrangements in eEF2 from Structure I through Structure V provide insights into the mechanisms of eEF2 association with the pre-translocation ribosome and dissociation from the post-translocation ribosome.	DISCUSS
12	22	structures	evidence	In all five structures, the GTPase domain is attached to the P stalk and the sarcin-ricin loop.	DISCUSS
28	41	GTPase domain	structure_element	In all five structures, the GTPase domain is attached to the P stalk and the sarcin-ricin loop.	DISCUSS
61	68	P stalk	structure_element	In all five structures, the GTPase domain is attached to the P stalk and the sarcin-ricin loop.	DISCUSS
77	94	sarcin-ricin loop	structure_element	In all five structures, the GTPase domain is attached to the P stalk and the sarcin-ricin loop.	DISCUSS
7	20	fully-rotated	protein_state	In the fully-rotated pre-translocation-like Structure I, an additional interaction exists.	DISCUSS
21	38	pre-translocation	protein_state	In the fully-rotated pre-translocation-like Structure I, an additional interaction exists.	DISCUSS
44	55	Structure I	evidence	In the fully-rotated pre-translocation-like Structure I, an additional interaction exists.	DISCUSS
6	19	switch loop I	structure_element	Here, switch loop I interacts with helix 14 (415CAAA418) of the 18S rRNA.	DISCUSS
35	43	helix 14	structure_element	Here, switch loop I interacts with helix 14 (415CAAA418) of the 18S rRNA.	DISCUSS
45	55	415CAAA418	structure_element	Here, switch loop I interacts with helix 14 (415CAAA418) of the 18S rRNA.	DISCUSS
64	72	18S rRNA	chemical	Here, switch loop I interacts with helix 14 (415CAAA418) of the 18S rRNA.	DISCUSS
31	44	GTPase center	site	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
56	65	GTP-bound	protein_state	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
115	136	translational GTPases	protein_type	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
144	155	presence of	protein_state	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
156	159	GTP	chemical	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
179	187	80S•eEF2	complex_assembly	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
196	206	bound with	protein_state	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
232	241	GDP•AlF4–	complex_assembly	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
247	258	switch loop	structure_element	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
280	284	A416	residue_name_number	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
286	296	invariable	protein_state	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
297	301	A344	residue_name_number	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
305	312	E. coli	species	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
317	321	A463	residue_name_number	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
325	335	H. sapiens	species	This stabilization renders the GTPase center to adopt a GTP-bound conformation, similar to those observed in other translational GTPases in the presence of GTP analogs and in the 80S•eEF2 complex bound with a transition-state mimic GDP•AlF4–. The switch loop contacts the base of A416 (invariable A344 in E. coli and A463 in H. sapiens).	DISCUSS
0	9	Mutations	experimental_method	Mutations of residues flanking A344 in E. coli 16S rRNA modestly inhibit translation but do not specifically affect EF-G-mediated translocation.	DISCUSS
31	35	A344	residue_name_number	Mutations of residues flanking A344 in E. coli 16S rRNA modestly inhibit translation but do not specifically affect EF-G-mediated translocation.	DISCUSS
39	46	E. coli	species	Mutations of residues flanking A344 in E. coli 16S rRNA modestly inhibit translation but do not specifically affect EF-G-mediated translocation.	DISCUSS
47	55	16S rRNA	chemical	Mutations of residues flanking A344 in E. coli 16S rRNA modestly inhibit translation but do not specifically affect EF-G-mediated translocation.	DISCUSS
116	120	EF-G	protein	Mutations of residues flanking A344 in E. coli 16S rRNA modestly inhibit translation but do not specifically affect EF-G-mediated translocation.	DISCUSS
23	27	A344	residue_name_number	However, the effect of A344 mutation on translation was not addressed in that study, leaving the question open whether this residue is critical for eEF2/EF-G function.	DISCUSS
28	36	mutation	experimental_method	However, the effect of A344 mutation on translation was not addressed in that study, leaving the question open whether this residue is critical for eEF2/EF-G function.	DISCUSS
148	152	eEF2	protein	However, the effect of A344 mutation on translation was not addressed in that study, leaving the question open whether this residue is critical for eEF2/EF-G function.	DISCUSS
153	157	EF-G	protein	However, the effect of A344 mutation on translation was not addressed in that study, leaving the question open whether this residue is critical for eEF2/EF-G function.	DISCUSS
24	27	h14	structure_element	The interaction between h14 and switch loop I is not resolved in Structures II to V, in all of which the small subunit is partially rotated or non-rotated, so that helix 14 is placed at least 6 Å farther from eEF2 (Figure 5d).	DISCUSS
32	45	switch loop I	structure_element	The interaction between h14 and switch loop I is not resolved in Structures II to V, in all of which the small subunit is partially rotated or non-rotated, so that helix 14 is placed at least 6 Å farther from eEF2 (Figure 5d).	DISCUSS
65	83	Structures II to V	evidence	The interaction between h14 and switch loop I is not resolved in Structures II to V, in all of which the small subunit is partially rotated or non-rotated, so that helix 14 is placed at least 6 Å farther from eEF2 (Figure 5d).	DISCUSS
105	118	small subunit	structure_element	The interaction between h14 and switch loop I is not resolved in Structures II to V, in all of which the small subunit is partially rotated or non-rotated, so that helix 14 is placed at least 6 Å farther from eEF2 (Figure 5d).	DISCUSS
122	139	partially rotated	protein_state	The interaction between h14 and switch loop I is not resolved in Structures II to V, in all of which the small subunit is partially rotated or non-rotated, so that helix 14 is placed at least 6 Å farther from eEF2 (Figure 5d).	DISCUSS
143	154	non-rotated	protein_state	The interaction between h14 and switch loop I is not resolved in Structures II to V, in all of which the small subunit is partially rotated or non-rotated, so that helix 14 is placed at least 6 Å farther from eEF2 (Figure 5d).	DISCUSS
164	172	helix 14	structure_element	The interaction between h14 and switch loop I is not resolved in Structures II to V, in all of which the small subunit is partially rotated or non-rotated, so that helix 14 is placed at least 6 Å farther from eEF2 (Figure 5d).	DISCUSS
209	213	eEF2	protein	The interaction between h14 and switch loop I is not resolved in Structures II to V, in all of which the small subunit is partially rotated or non-rotated, so that helix 14 is placed at least 6 Å farther from eEF2 (Figure 5d).	DISCUSS
51	59	ribosome	complex_assembly	We conclude that unlike other conformations of the ribosome, the fully rotated 40S subunit of the pre-translocation ribosome provides an interaction surface, complementing the P stalk and SRL, for binding of the GTP-bound translocase.	DISCUSS
65	78	fully rotated	protein_state	We conclude that unlike other conformations of the ribosome, the fully rotated 40S subunit of the pre-translocation ribosome provides an interaction surface, complementing the P stalk and SRL, for binding of the GTP-bound translocase.	DISCUSS
79	82	40S	complex_assembly	We conclude that unlike other conformations of the ribosome, the fully rotated 40S subunit of the pre-translocation ribosome provides an interaction surface, complementing the P stalk and SRL, for binding of the GTP-bound translocase.	DISCUSS
83	90	subunit	structure_element	We conclude that unlike other conformations of the ribosome, the fully rotated 40S subunit of the pre-translocation ribosome provides an interaction surface, complementing the P stalk and SRL, for binding of the GTP-bound translocase.	DISCUSS
98	115	pre-translocation	protein_state	We conclude that unlike other conformations of the ribosome, the fully rotated 40S subunit of the pre-translocation ribosome provides an interaction surface, complementing the P stalk and SRL, for binding of the GTP-bound translocase.	DISCUSS
116	124	ribosome	complex_assembly	We conclude that unlike other conformations of the ribosome, the fully rotated 40S subunit of the pre-translocation ribosome provides an interaction surface, complementing the P stalk and SRL, for binding of the GTP-bound translocase.	DISCUSS
137	156	interaction surface	site	We conclude that unlike other conformations of the ribosome, the fully rotated 40S subunit of the pre-translocation ribosome provides an interaction surface, complementing the P stalk and SRL, for binding of the GTP-bound translocase.	DISCUSS
176	183	P stalk	structure_element	We conclude that unlike other conformations of the ribosome, the fully rotated 40S subunit of the pre-translocation ribosome provides an interaction surface, complementing the P stalk and SRL, for binding of the GTP-bound translocase.	DISCUSS
188	191	SRL	structure_element	We conclude that unlike other conformations of the ribosome, the fully rotated 40S subunit of the pre-translocation ribosome provides an interaction surface, complementing the P stalk and SRL, for binding of the GTP-bound translocase.	DISCUSS
212	221	GTP-bound	protein_state	We conclude that unlike other conformations of the ribosome, the fully rotated 40S subunit of the pre-translocation ribosome provides an interaction surface, complementing the P stalk and SRL, for binding of the GTP-bound translocase.	DISCUSS
222	233	translocase	protein_type	We conclude that unlike other conformations of the ribosome, the fully rotated 40S subunit of the pre-translocation ribosome provides an interaction surface, complementing the P stalk and SRL, for binding of the GTP-bound translocase.	DISCUSS
85	92	rotated	protein_state	This structural basis rationalizes the observation of transient stabilization of the rotated 70S ribosome upon EF-G•GTP binding and prior to translocation.	DISCUSS
93	105	70S ribosome	complex_assembly	This structural basis rationalizes the observation of transient stabilization of the rotated 70S ribosome upon EF-G•GTP binding and prior to translocation.	DISCUSS
111	119	EF-G•GTP	complex_assembly	This structural basis rationalizes the observation of transient stabilization of the rotated 70S ribosome upon EF-G•GTP binding and prior to translocation.	DISCUSS
4	17	least rotated	protein_state	The least rotated conformation of the post-translocation Structure V suggests conformational changes that may trigger eEF2 release from the ribosome at the end of translocation.	DISCUSS
38	56	post-translocation	protein_state	The least rotated conformation of the post-translocation Structure V suggests conformational changes that may trigger eEF2 release from the ribosome at the end of translocation.	DISCUSS
57	68	Structure V	evidence	The least rotated conformation of the post-translocation Structure V suggests conformational changes that may trigger eEF2 release from the ribosome at the end of translocation.	DISCUSS
118	122	eEF2	protein	The least rotated conformation of the post-translocation Structure V suggests conformational changes that may trigger eEF2 release from the ribosome at the end of translocation.	DISCUSS
140	148	ribosome	complex_assembly	The least rotated conformation of the post-translocation Structure V suggests conformational changes that may trigger eEF2 release from the ribosome at the end of translocation.	DISCUSS
50	54	eEF2	protein	The most pronounced inter-domain rearrangement in eEF2 involves movement of domain III.	DISCUSS
83	86	III	structure_element	The most pronounced inter-domain rearrangement in eEF2 involves movement of domain III.	DISCUSS
7	14	rotated	protein_state	In the rotated or mid-rotated Structures I through III, this domain remains rigidly associated with domain V and the N-terminal superdomain and does not undergo noticeable rearrangements.	DISCUSS
18	29	mid-rotated	protein_state	In the rotated or mid-rotated Structures I through III, this domain remains rigidly associated with domain V and the N-terminal superdomain and does not undergo noticeable rearrangements.	DISCUSS
30	54	Structures I through III	evidence	In the rotated or mid-rotated Structures I through III, this domain remains rigidly associated with domain V and the N-terminal superdomain and does not undergo noticeable rearrangements.	DISCUSS
107	108	V	structure_element	In the rotated or mid-rotated Structures I through III, this domain remains rigidly associated with domain V and the N-terminal superdomain and does not undergo noticeable rearrangements.	DISCUSS
128	139	superdomain	structure_element	In the rotated or mid-rotated Structures I through III, this domain remains rigidly associated with domain V and the N-terminal superdomain and does not undergo noticeable rearrangements.	DISCUSS
3	14	Structure V	evidence	In Structure V, however, the tip of helix A of domain III is displaced toward domain I by ~5 Å relative to that in mid-rotated or fully rotated structures.	DISCUSS
36	43	helix A	structure_element	In Structure V, however, the tip of helix A of domain III is displaced toward domain I by ~5 Å relative to that in mid-rotated or fully rotated structures.	DISCUSS
54	57	III	structure_element	In Structure V, however, the tip of helix A of domain III is displaced toward domain I by ~5 Å relative to that in mid-rotated or fully rotated structures.	DISCUSS
85	86	I	structure_element	In Structure V, however, the tip of helix A of domain III is displaced toward domain I by ~5 Å relative to that in mid-rotated or fully rotated structures.	DISCUSS
115	126	mid-rotated	protein_state	In Structure V, however, the tip of helix A of domain III is displaced toward domain I by ~5 Å relative to that in mid-rotated or fully rotated structures.	DISCUSS
130	143	fully rotated	protein_state	In Structure V, however, the tip of helix A of domain III is displaced toward domain I by ~5 Å relative to that in mid-rotated or fully rotated structures.	DISCUSS
144	154	structures	evidence	In Structure V, however, the tip of helix A of domain III is displaced toward domain I by ~5 Å relative to that in mid-rotated or fully rotated structures.	DISCUSS
55	58	40S	complex_assembly	This displacement is caused by the 8 Å movement of the 40S body protein uS12 upon reverse intersubunit rotation from Structure I to V (Figure 6d).	DISCUSS
59	63	body	structure_element	This displacement is caused by the 8 Å movement of the 40S body protein uS12 upon reverse intersubunit rotation from Structure I to V (Figure 6d).	DISCUSS
72	76	uS12	protein	This displacement is caused by the 8 Å movement of the 40S body protein uS12 upon reverse intersubunit rotation from Structure I to V (Figure 6d).	DISCUSS
117	133	Structure I to V	evidence	This displacement is caused by the 8 Å movement of the 40S body protein uS12 upon reverse intersubunit rotation from Structure I to V (Figure 6d).	DISCUSS
36	39	III	structure_element	We propose that the shift of domain III by uS12 initiates intra-domain rearrangements in eEF2, which unstack the β-platform of domain III from that of domain V. This would result in a conformation characteristic of free eEF2 and EF-G in which the β-platforms are nearly perpendicular.	DISCUSS
43	47	uS12	protein	We propose that the shift of domain III by uS12 initiates intra-domain rearrangements in eEF2, which unstack the β-platform of domain III from that of domain V. This would result in a conformation characteristic of free eEF2 and EF-G in which the β-platforms are nearly perpendicular.	DISCUSS
89	93	eEF2	protein	We propose that the shift of domain III by uS12 initiates intra-domain rearrangements in eEF2, which unstack the β-platform of domain III from that of domain V. This would result in a conformation characteristic of free eEF2 and EF-G in which the β-platforms are nearly perpendicular.	DISCUSS
113	123	β-platform	structure_element	We propose that the shift of domain III by uS12 initiates intra-domain rearrangements in eEF2, which unstack the β-platform of domain III from that of domain V. This would result in a conformation characteristic of free eEF2 and EF-G in which the β-platforms are nearly perpendicular.	DISCUSS
134	137	III	structure_element	We propose that the shift of domain III by uS12 initiates intra-domain rearrangements in eEF2, which unstack the β-platform of domain III from that of domain V. This would result in a conformation characteristic of free eEF2 and EF-G in which the β-platforms are nearly perpendicular.	DISCUSS
158	159	V	structure_element	We propose that the shift of domain III by uS12 initiates intra-domain rearrangements in eEF2, which unstack the β-platform of domain III from that of domain V. This would result in a conformation characteristic of free eEF2 and EF-G in which the β-platforms are nearly perpendicular.	DISCUSS
215	219	free	protein_state	We propose that the shift of domain III by uS12 initiates intra-domain rearrangements in eEF2, which unstack the β-platform of domain III from that of domain V. This would result in a conformation characteristic of free eEF2 and EF-G in which the β-platforms are nearly perpendicular.	DISCUSS
220	224	eEF2	protein	We propose that the shift of domain III by uS12 initiates intra-domain rearrangements in eEF2, which unstack the β-platform of domain III from that of domain V. This would result in a conformation characteristic of free eEF2 and EF-G in which the β-platforms are nearly perpendicular.	DISCUSS
229	233	EF-G	protein	We propose that the shift of domain III by uS12 initiates intra-domain rearrangements in eEF2, which unstack the β-platform of domain III from that of domain V. This would result in a conformation characteristic of free eEF2 and EF-G in which the β-platforms are nearly perpendicular.	DISCUSS
247	258	β-platforms	structure_element	We propose that the shift of domain III by uS12 initiates intra-domain rearrangements in eEF2, which unstack the β-platform of domain III from that of domain V. This would result in a conformation characteristic of free eEF2 and EF-G in which the β-platforms are nearly perpendicular.	DISCUSS
21	32	Structure V	evidence	As we discuss below, Structure V captures a 'pre-unstacking' state due to stabilization of the interface between domains III and V by sordarin.	DISCUSS
45	59	pre-unstacking	protein_state	As we discuss below, Structure V captures a 'pre-unstacking' state due to stabilization of the interface between domains III and V by sordarin.	DISCUSS
95	104	interface	site	As we discuss below, Structure V captures a 'pre-unstacking' state due to stabilization of the interface between domains III and V by sordarin.	DISCUSS
121	124	III	structure_element	As we discuss below, Structure V captures a 'pre-unstacking' state due to stabilization of the interface between domains III and V by sordarin.	DISCUSS
129	130	V	structure_element	As we discuss below, Structure V captures a 'pre-unstacking' state due to stabilization of the interface between domains III and V by sordarin.	DISCUSS
134	142	sordarin	chemical	As we discuss below, Structure V captures a 'pre-unstacking' state due to stabilization of the interface between domains III and V by sordarin.	DISCUSS
0	8	Sordarin	chemical	Sordarin stabilizes GDP-bound eEF2 on the ribosome	DISCUSS
20	29	GDP-bound	protein_state	Sordarin stabilizes GDP-bound eEF2 on the ribosome	DISCUSS
30	34	eEF2	protein	Sordarin stabilizes GDP-bound eEF2 on the ribosome	DISCUSS
42	50	ribosome	complex_assembly	Sordarin stabilizes GDP-bound eEF2 on the ribosome	DISCUSS
0	8	Sordarin	chemical	Sordarin is a potent antifungal antibiotic that inhibits translation.	DISCUSS
9	32	biochemical experiments	experimental_method	Based on biochemical experiments, two alternative mechanisms of action were proposed: sordarin either prevents eEF2 departure by inhibiting GTP hydrolysis or acts after GTP hydrolysis.	DISCUSS
86	94	sordarin	chemical	Based on biochemical experiments, two alternative mechanisms of action were proposed: sordarin either prevents eEF2 departure by inhibiting GTP hydrolysis or acts after GTP hydrolysis.	DISCUSS
111	115	eEF2	protein	Based on biochemical experiments, two alternative mechanisms of action were proposed: sordarin either prevents eEF2 departure by inhibiting GTP hydrolysis or acts after GTP hydrolysis.	DISCUSS
140	143	GTP	chemical	Based on biochemical experiments, two alternative mechanisms of action were proposed: sordarin either prevents eEF2 departure by inhibiting GTP hydrolysis or acts after GTP hydrolysis.	DISCUSS
169	172	GTP	chemical	Based on biochemical experiments, two alternative mechanisms of action were proposed: sordarin either prevents eEF2 departure by inhibiting GTP hydrolysis or acts after GTP hydrolysis.	DISCUSS
41	49	eEF2•GTP	complex_assembly	Although our complex was assembled using eEF2•GTP, density maps clearly show GDP and Mg2+ in each structure (Figure 5g).	DISCUSS
51	63	density maps	evidence	Although our complex was assembled using eEF2•GTP, density maps clearly show GDP and Mg2+ in each structure (Figure 5g).	DISCUSS
77	80	GDP	chemical	Although our complex was assembled using eEF2•GTP, density maps clearly show GDP and Mg2+ in each structure (Figure 5g).	DISCUSS
85	89	Mg2+	chemical	Although our complex was assembled using eEF2•GTP, density maps clearly show GDP and Mg2+ in each structure (Figure 5g).	DISCUSS
98	107	structure	evidence	Although our complex was assembled using eEF2•GTP, density maps clearly show GDP and Mg2+ in each structure (Figure 5g).	DISCUSS
4	14	structures	evidence	Our structures therefore indicate that sordarin stalls eEF2 on the ribosome in the GDP-bound form, i.e. following GTP hydrolysis and phosphate release.	DISCUSS
39	47	sordarin	chemical	Our structures therefore indicate that sordarin stalls eEF2 on the ribosome in the GDP-bound form, i.e. following GTP hydrolysis and phosphate release.	DISCUSS
55	59	eEF2	protein	Our structures therefore indicate that sordarin stalls eEF2 on the ribosome in the GDP-bound form, i.e. following GTP hydrolysis and phosphate release.	DISCUSS
67	75	ribosome	complex_assembly	Our structures therefore indicate that sordarin stalls eEF2 on the ribosome in the GDP-bound form, i.e. following GTP hydrolysis and phosphate release.	DISCUSS
83	92	GDP-bound	protein_state	Our structures therefore indicate that sordarin stalls eEF2 on the ribosome in the GDP-bound form, i.e. following GTP hydrolysis and phosphate release.	DISCUSS
114	117	GTP	chemical	Our structures therefore indicate that sordarin stalls eEF2 on the ribosome in the GDP-bound form, i.e. following GTP hydrolysis and phosphate release.	DISCUSS
56	73	pre-translocation	protein_state	The mechanism of stalling is suggested by comparison of pre-translocation and post-translocation structures in our ensemble.	DISCUSS
78	96	post-translocation	protein_state	The mechanism of stalling is suggested by comparison of pre-translocation and post-translocation structures in our ensemble.	DISCUSS
97	107	structures	evidence	The mechanism of stalling is suggested by comparison of pre-translocation and post-translocation structures in our ensemble.	DISCUSS
12	22	structures	evidence	In all five structures, sordarin is bound between domains III and V of eEF2, stabilized by hydrophobic interactions identical to those in the isolated eEF2•sordarin complex (Figures 5g and h).	DISCUSS
24	32	sordarin	chemical	In all five structures, sordarin is bound between domains III and V of eEF2, stabilized by hydrophobic interactions identical to those in the isolated eEF2•sordarin complex (Figures 5g and h).	DISCUSS
36	41	bound	protein_state	In all five structures, sordarin is bound between domains III and V of eEF2, stabilized by hydrophobic interactions identical to those in the isolated eEF2•sordarin complex (Figures 5g and h).	DISCUSS
58	61	III	structure_element	In all five structures, sordarin is bound between domains III and V of eEF2, stabilized by hydrophobic interactions identical to those in the isolated eEF2•sordarin complex (Figures 5g and h).	DISCUSS
66	67	V	structure_element	In all five structures, sordarin is bound between domains III and V of eEF2, stabilized by hydrophobic interactions identical to those in the isolated eEF2•sordarin complex (Figures 5g and h).	DISCUSS
71	75	eEF2	protein	In all five structures, sordarin is bound between domains III and V of eEF2, stabilized by hydrophobic interactions identical to those in the isolated eEF2•sordarin complex (Figures 5g and h).	DISCUSS
91	115	hydrophobic interactions	bond_interaction	In all five structures, sordarin is bound between domains III and V of eEF2, stabilized by hydrophobic interactions identical to those in the isolated eEF2•sordarin complex (Figures 5g and h).	DISCUSS
142	150	isolated	protein_state	In all five structures, sordarin is bound between domains III and V of eEF2, stabilized by hydrophobic interactions identical to those in the isolated eEF2•sordarin complex (Figures 5g and h).	DISCUSS
151	164	eEF2•sordarin	complex_assembly	In all five structures, sordarin is bound between domains III and V of eEF2, stabilized by hydrophobic interactions identical to those in the isolated eEF2•sordarin complex (Figures 5g and h).	DISCUSS
7	25	nearly non-rotated	protein_state	In the nearly non-rotated post-translocation Structure V, the tip of domain III is shifted, however the interface between domains III and V remains unchanged, suggesting strong stabilization of this interface by sordarin.	DISCUSS
26	44	post-translocation	protein_state	In the nearly non-rotated post-translocation Structure V, the tip of domain III is shifted, however the interface between domains III and V remains unchanged, suggesting strong stabilization of this interface by sordarin.	DISCUSS
45	56	Structure V	evidence	In the nearly non-rotated post-translocation Structure V, the tip of domain III is shifted, however the interface between domains III and V remains unchanged, suggesting strong stabilization of this interface by sordarin.	DISCUSS
76	79	III	structure_element	In the nearly non-rotated post-translocation Structure V, the tip of domain III is shifted, however the interface between domains III and V remains unchanged, suggesting strong stabilization of this interface by sordarin.	DISCUSS
104	113	interface	site	In the nearly non-rotated post-translocation Structure V, the tip of domain III is shifted, however the interface between domains III and V remains unchanged, suggesting strong stabilization of this interface by sordarin.	DISCUSS
130	133	III	structure_element	In the nearly non-rotated post-translocation Structure V, the tip of domain III is shifted, however the interface between domains III and V remains unchanged, suggesting strong stabilization of this interface by sordarin.	DISCUSS
138	139	V	structure_element	In the nearly non-rotated post-translocation Structure V, the tip of domain III is shifted, however the interface between domains III and V remains unchanged, suggesting strong stabilization of this interface by sordarin.	DISCUSS
199	208	interface	site	In the nearly non-rotated post-translocation Structure V, the tip of domain III is shifted, however the interface between domains III and V remains unchanged, suggesting strong stabilization of this interface by sordarin.	DISCUSS
212	220	sordarin	chemical	In the nearly non-rotated post-translocation Structure V, the tip of domain III is shifted, however the interface between domains III and V remains unchanged, suggesting strong stabilization of this interface by sordarin.	DISCUSS
13	24	Structure V	evidence	We note that Structure V is slightly more rotated than the 80S•2tRNA•mRNA complex in the absence of eEF2•sordarin, implying that sordarin interferes with the final stages of reverse rotation of the post-translocation ribosome.	DISCUSS
59	73	80S•2tRNA•mRNA	complex_assembly	We note that Structure V is slightly more rotated than the 80S•2tRNA•mRNA complex in the absence of eEF2•sordarin, implying that sordarin interferes with the final stages of reverse rotation of the post-translocation ribosome.	DISCUSS
89	99	absence of	protein_state	We note that Structure V is slightly more rotated than the 80S•2tRNA•mRNA complex in the absence of eEF2•sordarin, implying that sordarin interferes with the final stages of reverse rotation of the post-translocation ribosome.	DISCUSS
100	113	eEF2•sordarin	complex_assembly	We note that Structure V is slightly more rotated than the 80S•2tRNA•mRNA complex in the absence of eEF2•sordarin, implying that sordarin interferes with the final stages of reverse rotation of the post-translocation ribosome.	DISCUSS
129	137	sordarin	chemical	We note that Structure V is slightly more rotated than the 80S•2tRNA•mRNA complex in the absence of eEF2•sordarin, implying that sordarin interferes with the final stages of reverse rotation of the post-translocation ribosome.	DISCUSS
198	216	post-translocation	protein_state	We note that Structure V is slightly more rotated than the 80S•2tRNA•mRNA complex in the absence of eEF2•sordarin, implying that sordarin interferes with the final stages of reverse rotation of the post-translocation ribosome.	DISCUSS
217	225	ribosome	complex_assembly	We note that Structure V is slightly more rotated than the 80S•2tRNA•mRNA complex in the absence of eEF2•sordarin, implying that sordarin interferes with the final stages of reverse rotation of the post-translocation ribosome.	DISCUSS
16	24	sordarin	chemical	We propose that sordarin acts to prevent full reverse rotation and release of eEF2•GDP by stabilizing the interdomain interface and thus blocking uS12-induced disengagement of domain III from domain V.	DISCUSS
78	86	eEF2•GDP	complex_assembly	We propose that sordarin acts to prevent full reverse rotation and release of eEF2•GDP by stabilizing the interdomain interface and thus blocking uS12-induced disengagement of domain III from domain V.	DISCUSS
106	127	interdomain interface	site	We propose that sordarin acts to prevent full reverse rotation and release of eEF2•GDP by stabilizing the interdomain interface and thus blocking uS12-induced disengagement of domain III from domain V.	DISCUSS
146	150	uS12	protein	We propose that sordarin acts to prevent full reverse rotation and release of eEF2•GDP by stabilizing the interdomain interface and thus blocking uS12-induced disengagement of domain III from domain V.	DISCUSS
183	186	III	structure_element	We propose that sordarin acts to prevent full reverse rotation and release of eEF2•GDP by stabilizing the interdomain interface and thus blocking uS12-induced disengagement of domain III from domain V.	DISCUSS
199	200	V	structure_element	We propose that sordarin acts to prevent full reverse rotation and release of eEF2•GDP by stabilizing the interdomain interface and thus blocking uS12-induced disengagement of domain III from domain V.	DISCUSS
17	21	tRNA	chemical	Implications for tRNA and mRNA translocation during translation	DISCUSS
26	30	mRNA	chemical	Implications for tRNA and mRNA translocation during translation	DISCUSS
25	29	tRNA	chemical	Because translocation of tRNA must involve large-scale dynamics, this step has long been regarded as the most puzzling step of translation.	DISCUSS
32	36	tRNA	chemical	Intersubunit rearrangements and tRNA hybrid states have been proposed to play key roles half a century ago.	DISCUSS
37	43	hybrid	protein_state	Intersubunit rearrangements and tRNA hybrid states have been proposed to play key roles half a century ago.	DISCUSS
22	26	body	structure_element	Despite an impressive body of biochemical, fluorescence and structural data accumulated since then, translocation remains the least understood step of elongation.	DISCUSS
30	75	biochemical, fluorescence and structural data	evidence	Despite an impressive body of biochemical, fluorescence and structural data accumulated since then, translocation remains the least understood step of elongation.	DISCUSS
32	40	ribosome	complex_assembly	The structural understanding of ribosome and tRNA dynamics has been greatly aided by a wealth of X-ray and cryo-EM structures (reviewed in).	DISCUSS
45	49	tRNA	chemical	The structural understanding of ribosome and tRNA dynamics has been greatly aided by a wealth of X-ray and cryo-EM structures (reviewed in).	DISCUSS
97	102	X-ray	experimental_method	The structural understanding of ribosome and tRNA dynamics has been greatly aided by a wealth of X-ray and cryo-EM structures (reviewed in).	DISCUSS
107	114	cryo-EM	experimental_method	The structural understanding of ribosome and tRNA dynamics has been greatly aided by a wealth of X-ray and cryo-EM structures (reviewed in).	DISCUSS
115	125	structures	evidence	The structural understanding of ribosome and tRNA dynamics has been greatly aided by a wealth of X-ray and cryo-EM structures (reviewed in).	DISCUSS
30	34	eEF2	protein	However, visualization of the eEF2/EF-G-induced translocation is confined to very early pre-EF-G-entry states and late (almost translocated or fully translocated) states, leaving most of the path from the A to the P site uncharacterized (Figure 1—figure supplement 1).	DISCUSS
35	39	EF-G	protein	However, visualization of the eEF2/EF-G-induced translocation is confined to very early pre-EF-G-entry states and late (almost translocated or fully translocated) states, leaving most of the path from the A to the P site uncharacterized (Figure 1—figure supplement 1).	DISCUSS
88	102	pre-EF-G-entry	protein_state	However, visualization of the eEF2/EF-G-induced translocation is confined to very early pre-EF-G-entry states and late (almost translocated or fully translocated) states, leaving most of the path from the A to the P site uncharacterized (Figure 1—figure supplement 1).	DISCUSS
120	139	almost translocated	protein_state	However, visualization of the eEF2/EF-G-induced translocation is confined to very early pre-EF-G-entry states and late (almost translocated or fully translocated) states, leaving most of the path from the A to the P site uncharacterized (Figure 1—figure supplement 1).	DISCUSS
143	161	fully translocated	protein_state	However, visualization of the eEF2/EF-G-induced translocation is confined to very early pre-EF-G-entry states and late (almost translocated or fully translocated) states, leaving most of the path from the A to the P site uncharacterized (Figure 1—figure supplement 1).	DISCUSS
205	220	A to the P site	site	However, visualization of the eEF2/EF-G-induced translocation is confined to very early pre-EF-G-entry states and late (almost translocated or fully translocated) states, leaving most of the path from the A to the P site uncharacterized (Figure 1—figure supplement 1).	DISCUSS
69	73	tRNA	chemical	Our study provides new insights into the structural understanding of tRNA translocation.	DISCUSS
23	27	tRNA	chemical	First, we propose that tRNA and IRES translocations occur via the same general trajectory.	DISCUSS
32	36	IRES	site	First, we propose that tRNA and IRES translocations occur via the same general trajectory.	DISCUSS
35	43	ribosome	complex_assembly	This is evident from the fact that ribosome rearrangements in translocation are inherent to the ribosome and likely occur in similar ways in both cases.	DISCUSS
96	104	ribosome	complex_assembly	This is evident from the fact that ribosome rearrangements in translocation are inherent to the ribosome and likely occur in similar ways in both cases.	DISCUSS
39	47	ribosome	complex_assembly	Furthermore, the step-wise coupling of ribosome dynamics with IRES translocation is overall consistent with that observed for 2tRNA•mRNA translocation in solution.	DISCUSS
62	66	IRES	site	Furthermore, the step-wise coupling of ribosome dynamics with IRES translocation is overall consistent with that observed for 2tRNA•mRNA translocation in solution.	DISCUSS
126	136	2tRNA•mRNA	complex_assembly	Furthermore, the step-wise coupling of ribosome dynamics with IRES translocation is overall consistent with that observed for 2tRNA•mRNA translocation in solution.	DISCUSS
13	49	fluorescence and biochemical studies	experimental_method	For example, fluorescence and biochemical studies revealed that the early pre-translocation EF-G-bound ribosomes are fully rotated and translocation of the tRNA-mRNA complex occurs during reverse rotation of the small subunit, coupled with head swivel.	DISCUSS
74	91	pre-translocation	protein_state	For example, fluorescence and biochemical studies revealed that the early pre-translocation EF-G-bound ribosomes are fully rotated and translocation of the tRNA-mRNA complex occurs during reverse rotation of the small subunit, coupled with head swivel.	DISCUSS
92	102	EF-G-bound	protein_state	For example, fluorescence and biochemical studies revealed that the early pre-translocation EF-G-bound ribosomes are fully rotated and translocation of the tRNA-mRNA complex occurs during reverse rotation of the small subunit, coupled with head swivel.	DISCUSS
103	112	ribosomes	complex_assembly	For example, fluorescence and biochemical studies revealed that the early pre-translocation EF-G-bound ribosomes are fully rotated and translocation of the tRNA-mRNA complex occurs during reverse rotation of the small subunit, coupled with head swivel.	DISCUSS
117	130	fully rotated	protein_state	For example, fluorescence and biochemical studies revealed that the early pre-translocation EF-G-bound ribosomes are fully rotated and translocation of the tRNA-mRNA complex occurs during reverse rotation of the small subunit, coupled with head swivel.	DISCUSS
156	165	tRNA-mRNA	complex_assembly	For example, fluorescence and biochemical studies revealed that the early pre-translocation EF-G-bound ribosomes are fully rotated and translocation of the tRNA-mRNA complex occurs during reverse rotation of the small subunit, coupled with head swivel.	DISCUSS
212	225	small subunit	structure_element	For example, fluorescence and biochemical studies revealed that the early pre-translocation EF-G-bound ribosomes are fully rotated and translocation of the tRNA-mRNA complex occurs during reverse rotation of the small subunit, coupled with head swivel.	DISCUSS
240	244	head	structure_element	For example, fluorescence and biochemical studies revealed that the early pre-translocation EF-G-bound ribosomes are fully rotated and translocation of the tRNA-mRNA complex occurs during reverse rotation of the small subunit, coupled with head swivel.	DISCUSS
16	24	ribosome	complex_assembly	The sequence of ribosome rearrangements during IRES translocation also agrees with that inferred from 70S•EF-G structures, including those in which the A-to-P-site translocating tRNA was not present.	DISCUSS
47	51	IRES	site	The sequence of ribosome rearrangements during IRES translocation also agrees with that inferred from 70S•EF-G structures, including those in which the A-to-P-site translocating tRNA was not present.	DISCUSS
102	110	70S•EF-G	complex_assembly	The sequence of ribosome rearrangements during IRES translocation also agrees with that inferred from 70S•EF-G structures, including those in which the A-to-P-site translocating tRNA was not present.	DISCUSS
111	121	structures	evidence	The sequence of ribosome rearrangements during IRES translocation also agrees with that inferred from 70S•EF-G structures, including those in which the A-to-P-site translocating tRNA was not present.	DISCUSS
152	163	A-to-P-site	site	The sequence of ribosome rearrangements during IRES translocation also agrees with that inferred from 70S•EF-G structures, including those in which the A-to-P-site translocating tRNA was not present.	DISCUSS
178	182	tRNA	chemical	The sequence of ribosome rearrangements during IRES translocation also agrees with that inferred from 70S•EF-G structures, including those in which the A-to-P-site translocating tRNA was not present.	DISCUSS
52	60	ribosome	complex_assembly	Specifically, an earlier translocation intermediate ribosome (TIpre) was proposed to adopt a rotated (7–9°) body and a partly rotated head (5–7.5°), in agreement with the conformation of our Structure I. The most swiveled head (18–21°) was observed in a mid-rotated ribosome (3–5°) of a later translocation intermediate TIpost, similar to the conformation of our Structure III.	DISCUSS
93	100	rotated	protein_state	Specifically, an earlier translocation intermediate ribosome (TIpre) was proposed to adopt a rotated (7–9°) body and a partly rotated head (5–7.5°), in agreement with the conformation of our Structure I. The most swiveled head (18–21°) was observed in a mid-rotated ribosome (3–5°) of a later translocation intermediate TIpost, similar to the conformation of our Structure III.	DISCUSS
108	112	body	structure_element	Specifically, an earlier translocation intermediate ribosome (TIpre) was proposed to adopt a rotated (7–9°) body and a partly rotated head (5–7.5°), in agreement with the conformation of our Structure I. The most swiveled head (18–21°) was observed in a mid-rotated ribosome (3–5°) of a later translocation intermediate TIpost, similar to the conformation of our Structure III.	DISCUSS
119	133	partly rotated	protein_state	Specifically, an earlier translocation intermediate ribosome (TIpre) was proposed to adopt a rotated (7–9°) body and a partly rotated head (5–7.5°), in agreement with the conformation of our Structure I. The most swiveled head (18–21°) was observed in a mid-rotated ribosome (3–5°) of a later translocation intermediate TIpost, similar to the conformation of our Structure III.	DISCUSS
134	138	head	structure_element	Specifically, an earlier translocation intermediate ribosome (TIpre) was proposed to adopt a rotated (7–9°) body and a partly rotated head (5–7.5°), in agreement with the conformation of our Structure I. The most swiveled head (18–21°) was observed in a mid-rotated ribosome (3–5°) of a later translocation intermediate TIpost, similar to the conformation of our Structure III.	DISCUSS
191	202	Structure I	evidence	Specifically, an earlier translocation intermediate ribosome (TIpre) was proposed to adopt a rotated (7–9°) body and a partly rotated head (5–7.5°), in agreement with the conformation of our Structure I. The most swiveled head (18–21°) was observed in a mid-rotated ribosome (3–5°) of a later translocation intermediate TIpost, similar to the conformation of our Structure III.	DISCUSS
208	221	most swiveled	protein_state	Specifically, an earlier translocation intermediate ribosome (TIpre) was proposed to adopt a rotated (7–9°) body and a partly rotated head (5–7.5°), in agreement with the conformation of our Structure I. The most swiveled head (18–21°) was observed in a mid-rotated ribosome (3–5°) of a later translocation intermediate TIpost, similar to the conformation of our Structure III.	DISCUSS
222	226	head	structure_element	Specifically, an earlier translocation intermediate ribosome (TIpre) was proposed to adopt a rotated (7–9°) body and a partly rotated head (5–7.5°), in agreement with the conformation of our Structure I. The most swiveled head (18–21°) was observed in a mid-rotated ribosome (3–5°) of a later translocation intermediate TIpost, similar to the conformation of our Structure III.	DISCUSS
254	265	mid-rotated	protein_state	Specifically, an earlier translocation intermediate ribosome (TIpre) was proposed to adopt a rotated (7–9°) body and a partly rotated head (5–7.5°), in agreement with the conformation of our Structure I. The most swiveled head (18–21°) was observed in a mid-rotated ribosome (3–5°) of a later translocation intermediate TIpost, similar to the conformation of our Structure III.	DISCUSS
266	274	ribosome	complex_assembly	Specifically, an earlier translocation intermediate ribosome (TIpre) was proposed to adopt a rotated (7–9°) body and a partly rotated head (5–7.5°), in agreement with the conformation of our Structure I. The most swiveled head (18–21°) was observed in a mid-rotated ribosome (3–5°) of a later translocation intermediate TIpost, similar to the conformation of our Structure III.	DISCUSS
363	376	Structure III	evidence	Specifically, an earlier translocation intermediate ribosome (TIpre) was proposed to adopt a rotated (7–9°) body and a partly rotated head (5–7.5°), in agreement with the conformation of our Structure I. The most swiveled head (18–21°) was observed in a mid-rotated ribosome (3–5°) of a later translocation intermediate TIpost, similar to the conformation of our Structure III.	DISCUSS
83	94	A-to-P-site	site	Overall, these correlations suggest that the intermediate locations of the elusive A-to-P-site translocating tRNA are similar to those of PKI in our structures.	DISCUSS
109	113	tRNA	chemical	Overall, these correlations suggest that the intermediate locations of the elusive A-to-P-site translocating tRNA are similar to those of PKI in our structures.	DISCUSS
138	141	PKI	structure_element	Overall, these correlations suggest that the intermediate locations of the elusive A-to-P-site translocating tRNA are similar to those of PKI in our structures.	DISCUSS
149	159	structures	evidence	Overall, these correlations suggest that the intermediate locations of the elusive A-to-P-site translocating tRNA are similar to those of PKI in our structures.	DISCUSS
12	22	structures	evidence	Second, the structures clarify the structural basis of the often-used but structurally undefined terms 'locking' and 'unlocking' with respect to the pre-translocation complex (Figure 6f).	DISCUSS
149	166	pre-translocation	protein_state	Second, the structures clarify the structural basis of the often-used but structurally undefined terms 'locking' and 'unlocking' with respect to the pre-translocation complex (Figure 6f).	DISCUSS
12	29	pre-translocation	protein_state	We deem the pre-translocation complex locked, because the A-site bound ASL-mRNA is stabilized by interactions with the decoding center.	DISCUSS
38	44	locked	protein_state	We deem the pre-translocation complex locked, because the A-site bound ASL-mRNA is stabilized by interactions with the decoding center.	DISCUSS
58	70	A-site bound	protein_state	We deem the pre-translocation complex locked, because the A-site bound ASL-mRNA is stabilized by interactions with the decoding center.	DISCUSS
75	79	mRNA	chemical	We deem the pre-translocation complex locked, because the A-site bound ASL-mRNA is stabilized by interactions with the decoding center.	DISCUSS
119	134	decoding center	site	We deem the pre-translocation complex locked, because the A-site bound ASL-mRNA is stabilized by interactions with the decoding center.	DISCUSS
42	51	classical	protein_state	These interactions are maintained for the classical- and hybrid-state tRNAs in the spontaneously sampled non-rotated and rotated ribosomes, respectively.	DISCUSS
57	63	hybrid	protein_state	These interactions are maintained for the classical- and hybrid-state tRNAs in the spontaneously sampled non-rotated and rotated ribosomes, respectively.	DISCUSS
70	75	tRNAs	chemical	These interactions are maintained for the classical- and hybrid-state tRNAs in the spontaneously sampled non-rotated and rotated ribosomes, respectively.	DISCUSS
105	116	non-rotated	protein_state	These interactions are maintained for the classical- and hybrid-state tRNAs in the spontaneously sampled non-rotated and rotated ribosomes, respectively.	DISCUSS
121	128	rotated	protein_state	These interactions are maintained for the classical- and hybrid-state tRNAs in the spontaneously sampled non-rotated and rotated ribosomes, respectively.	DISCUSS
129	138	ribosomes	complex_assembly	These interactions are maintained for the classical- and hybrid-state tRNAs in the spontaneously sampled non-rotated and rotated ribosomes, respectively.	DISCUSS
37	58	codon-anticodon helix	structure_element	Unlocking involves separation of the codon-anticodon helix from the decoding center residues by the protruding tip of eEF2/EF-G (Figure 7), occurring in the fully rotated ribosome at an early pre-translocation step.	DISCUSS
68	83	decoding center	site	Unlocking involves separation of the codon-anticodon helix from the decoding center residues by the protruding tip of eEF2/EF-G (Figure 7), occurring in the fully rotated ribosome at an early pre-translocation step.	DISCUSS
118	122	eEF2	protein	Unlocking involves separation of the codon-anticodon helix from the decoding center residues by the protruding tip of eEF2/EF-G (Figure 7), occurring in the fully rotated ribosome at an early pre-translocation step.	DISCUSS
123	127	EF-G	protein	Unlocking involves separation of the codon-anticodon helix from the decoding center residues by the protruding tip of eEF2/EF-G (Figure 7), occurring in the fully rotated ribosome at an early pre-translocation step.	DISCUSS
157	170	fully rotated	protein_state	Unlocking involves separation of the codon-anticodon helix from the decoding center residues by the protruding tip of eEF2/EF-G (Figure 7), occurring in the fully rotated ribosome at an early pre-translocation step.	DISCUSS
171	179	ribosome	complex_assembly	Unlocking involves separation of the codon-anticodon helix from the decoding center residues by the protruding tip of eEF2/EF-G (Figure 7), occurring in the fully rotated ribosome at an early pre-translocation step.	DISCUSS
192	209	pre-translocation	protein_state	Unlocking involves separation of the codon-anticodon helix from the decoding center residues by the protruding tip of eEF2/EF-G (Figure 7), occurring in the fully rotated ribosome at an early pre-translocation step.	DISCUSS
19	23	head	structure_element	This unlatches the head, allowing creation of hitherto elusive intermediate tRNA positions during spontaneous reverse body rotation.	DISCUSS
76	80	tRNA	chemical	This unlatches the head, allowing creation of hitherto elusive intermediate tRNA positions during spontaneous reverse body rotation.	DISCUSS
118	122	body	structure_element	This unlatches the head, allowing creation of hitherto elusive intermediate tRNA positions during spontaneous reverse body rotation.	DISCUSS
46	50	head	structure_element	Third, our findings uncover a new role of the head swivel.	DISCUSS
54	66	constriction	site	Previous studies showed that this movement widens the constriction ('gate') between the P and E sites, thus allowing the P-tRNA passage to the E site.	DISCUSS
69	73	gate	site	Previous studies showed that this movement widens the constriction ('gate') between the P and E sites, thus allowing the P-tRNA passage to the E site.	DISCUSS
88	101	P and E sites	site	Previous studies showed that this movement widens the constriction ('gate') between the P and E sites, thus allowing the P-tRNA passage to the E site.	DISCUSS
121	122	P	site	Previous studies showed that this movement widens the constriction ('gate') between the P and E sites, thus allowing the P-tRNA passage to the E site.	DISCUSS
123	127	tRNA	chemical	Previous studies showed that this movement widens the constriction ('gate') between the P and E sites, thus allowing the P-tRNA passage to the E site.	DISCUSS
143	149	E site	site	Previous studies showed that this movement widens the constriction ('gate') between the P and E sites, thus allowing the P-tRNA passage to the E site.	DISCUSS
20	24	gate	site	In addition to the 'gate-opening' role, we now show that the head swivel brings the head A site to the body P site, allowing a step-wise conveying of the codon-anticodon helix between the A and P sites.	DISCUSS
61	65	head	structure_element	In addition to the 'gate-opening' role, we now show that the head swivel brings the head A site to the body P site, allowing a step-wise conveying of the codon-anticodon helix between the A and P sites.	DISCUSS
84	88	head	structure_element	In addition to the 'gate-opening' role, we now show that the head swivel brings the head A site to the body P site, allowing a step-wise conveying of the codon-anticodon helix between the A and P sites.	DISCUSS
89	95	A site	site	In addition to the 'gate-opening' role, we now show that the head swivel brings the head A site to the body P site, allowing a step-wise conveying of the codon-anticodon helix between the A and P sites.	DISCUSS
103	107	body	structure_element	In addition to the 'gate-opening' role, we now show that the head swivel brings the head A site to the body P site, allowing a step-wise conveying of the codon-anticodon helix between the A and P sites.	DISCUSS
108	114	P site	site	In addition to the 'gate-opening' role, we now show that the head swivel brings the head A site to the body P site, allowing a step-wise conveying of the codon-anticodon helix between the A and P sites.	DISCUSS
154	175	codon-anticodon helix	structure_element	In addition to the 'gate-opening' role, we now show that the head swivel brings the head A site to the body P site, allowing a step-wise conveying of the codon-anticodon helix between the A and P sites.	DISCUSS
188	201	A and P sites	site	In addition to the 'gate-opening' role, we now show that the head swivel brings the head A site to the body P site, allowing a step-wise conveying of the codon-anticodon helix between the A and P sites.	DISCUSS
36	45	particles	experimental_method	Finally, the similar populations of particles (within a 2X range) in our 80S•IRES•eEF2 reconstructions (Figure 1—figure supplement 2) suggest that the intermediate translocation states sample several energetically similar and interconverting conformations.	DISCUSS
73	86	80S•IRES•eEF2	complex_assembly	Finally, the similar populations of particles (within a 2X range) in our 80S•IRES•eEF2 reconstructions (Figure 1—figure supplement 2) suggest that the intermediate translocation states sample several energetically similar and interconverting conformations.	DISCUSS
87	102	reconstructions	evidence	Finally, the similar populations of particles (within a 2X range) in our 80S•IRES•eEF2 reconstructions (Figure 1—figure supplement 2) suggest that the intermediate translocation states sample several energetically similar and interconverting conformations.	DISCUSS
156	164	ribosome	complex_assembly	This is consistent with the idea of a rather flat energy landscape of translocation, suggested by recent work that measured mechanical work produced by the ribosome during translocation.	DISCUSS
139	160	codon-anticodon helix	structure_element	Our findings implicate, however, that the energy landscape is not completely flat and contains local minima for transient positions of the codon-anticodon helix between the A and P sites.	DISCUSS
173	186	A and P sites	site	Our findings implicate, however, that the energy landscape is not completely flat and contains local minima for transient positions of the codon-anticodon helix between the A and P sites.	DISCUSS
17	20	PKI	structure_element	The shift of the PKI with respect to the body occurs during forward head swivel in two major sub-steps of ~4 Å each (initiation complex to I, and I to II), after which PKI undergoes small shifts to settle in the body P site in Structures III, IV and V (Figure 2—source data 1).	DISCUSS
41	45	body	structure_element	The shift of the PKI with respect to the body occurs during forward head swivel in two major sub-steps of ~4 Å each (initiation complex to I, and I to II), after which PKI undergoes small shifts to settle in the body P site in Structures III, IV and V (Figure 2—source data 1).	DISCUSS
68	72	head	structure_element	The shift of the PKI with respect to the body occurs during forward head swivel in two major sub-steps of ~4 Å each (initiation complex to I, and I to II), after which PKI undergoes small shifts to settle in the body P site in Structures III, IV and V (Figure 2—source data 1).	DISCUSS
117	135	initiation complex	complex_assembly	The shift of the PKI with respect to the body occurs during forward head swivel in two major sub-steps of ~4 Å each (initiation complex to I, and I to II), after which PKI undergoes small shifts to settle in the body P site in Structures III, IV and V (Figure 2—source data 1).	DISCUSS
139	140	I	evidence	The shift of the PKI with respect to the body occurs during forward head swivel in two major sub-steps of ~4 Å each (initiation complex to I, and I to II), after which PKI undergoes small shifts to settle in the body P site in Structures III, IV and V (Figure 2—source data 1).	DISCUSS
146	147	I	evidence	The shift of the PKI with respect to the body occurs during forward head swivel in two major sub-steps of ~4 Å each (initiation complex to I, and I to II), after which PKI undergoes small shifts to settle in the body P site in Structures III, IV and V (Figure 2—source data 1).	DISCUSS
151	153	II	evidence	The shift of the PKI with respect to the body occurs during forward head swivel in two major sub-steps of ~4 Å each (initiation complex to I, and I to II), after which PKI undergoes small shifts to settle in the body P site in Structures III, IV and V (Figure 2—source data 1).	DISCUSS
168	171	PKI	structure_element	The shift of the PKI with respect to the body occurs during forward head swivel in two major sub-steps of ~4 Å each (initiation complex to I, and I to II), after which PKI undergoes small shifts to settle in the body P site in Structures III, IV and V (Figure 2—source data 1).	DISCUSS
212	216	body	structure_element	The shift of the PKI with respect to the body occurs during forward head swivel in two major sub-steps of ~4 Å each (initiation complex to I, and I to II), after which PKI undergoes small shifts to settle in the body P site in Structures III, IV and V (Figure 2—source data 1).	DISCUSS
217	223	P site	site	The shift of the PKI with respect to the body occurs during forward head swivel in two major sub-steps of ~4 Å each (initiation complex to I, and I to II), after which PKI undergoes small shifts to settle in the body P site in Structures III, IV and V (Figure 2—source data 1).	DISCUSS
227	251	Structures III, IV and V	evidence	The shift of the PKI with respect to the body occurs during forward head swivel in two major sub-steps of ~4 Å each (initiation complex to I, and I to II), after which PKI undergoes small shifts to settle in the body P site in Structures III, IV and V (Figure 2—source data 1).	DISCUSS
12	15	PKI	structure_element	Movement of PKI relative to the head occurs during the subsequent reverse swivel in three 3–7 Å sub-steps (II to III to IV to V).	DISCUSS
32	36	head	structure_element	Movement of PKI relative to the head occurs during the subsequent reverse swivel in three 3–7 Å sub-steps (II to III to IV to V).	DISCUSS
107	127	II to III to IV to V	evidence	Movement of PKI relative to the head occurs during the subsequent reverse swivel in three 3–7 Å sub-steps (II to III to IV to V).	DISCUSS
48	52	maps	evidence	We note that four of our near-atomic resolution maps comprised ~30,000 particles each, the minimum number required for a near-atomic-resolution reconstruction of the ribosome.	DISCUSS
71	80	particles	experimental_method	We note that four of our near-atomic resolution maps comprised ~30,000 particles each, the minimum number required for a near-atomic-resolution reconstruction of the ribosome.	DISCUSS
121	158	near-atomic-resolution reconstruction	evidence	We note that four of our near-atomic resolution maps comprised ~30,000 particles each, the minimum number required for a near-atomic-resolution reconstruction of the ribosome.	DISCUSS
166	174	ribosome	complex_assembly	We note that four of our near-atomic resolution maps comprised ~30,000 particles each, the minimum number required for a near-atomic-resolution reconstruction of the ribosome.	DISCUSS
15	20	viral	taxonomy_domain	Translation of viral mRNA	DISCUSS
21	25	mRNA	chemical	Translation of viral mRNA	DISCUSS
80	83	IGR	structure_element	Our work sheds light on the dynamic mechanism of cap-independent translation by IGR IRESs, tightly coupled with the universally conserved dynamic properties of the ribosome.	DISCUSS
84	89	IRESs	site	Our work sheds light on the dynamic mechanism of cap-independent translation by IGR IRESs, tightly coupled with the universally conserved dynamic properties of the ribosome.	DISCUSS
116	137	universally conserved	protein_state	Our work sheds light on the dynamic mechanism of cap-independent translation by IGR IRESs, tightly coupled with the universally conserved dynamic properties of the ribosome.	DISCUSS
164	172	ribosome	complex_assembly	Our work sheds light on the dynamic mechanism of cap-independent translation by IGR IRESs, tightly coupled with the universally conserved dynamic properties of the ribosome.	DISCUSS
4	11	cryo-EM	experimental_method	The cryo-EM structures demonstrate that the TSV IRES structurally and dynamically represents a chimera of the 2tRNA•mRNA translocating complex (A/P-tRNA • P/E-tRNA • mRNA).	DISCUSS
12	22	structures	evidence	The cryo-EM structures demonstrate that the TSV IRES structurally and dynamically represents a chimera of the 2tRNA•mRNA translocating complex (A/P-tRNA • P/E-tRNA • mRNA).	DISCUSS
44	47	TSV	species	The cryo-EM structures demonstrate that the TSV IRES structurally and dynamically represents a chimera of the 2tRNA•mRNA translocating complex (A/P-tRNA • P/E-tRNA • mRNA).	DISCUSS
48	52	IRES	site	The cryo-EM structures demonstrate that the TSV IRES structurally and dynamically represents a chimera of the 2tRNA•mRNA translocating complex (A/P-tRNA • P/E-tRNA • mRNA).	DISCUSS
110	120	2tRNA•mRNA	complex_assembly	The cryo-EM structures demonstrate that the TSV IRES structurally and dynamically represents a chimera of the 2tRNA•mRNA translocating complex (A/P-tRNA • P/E-tRNA • mRNA).	DISCUSS
144	170	A/P-tRNA • P/E-tRNA • mRNA	complex_assembly	The cryo-EM structures demonstrate that the TSV IRES structurally and dynamically represents a chimera of the 2tRNA•mRNA translocating complex (A/P-tRNA • P/E-tRNA • mRNA).	DISCUSS
12	22	2tRNA•mRNA	complex_assembly	Like in the 2tRNA•mRNA translocating complex in which the two tRNAs move independently of each other, the PKI domain moves relative to the 5´-domain, causing the IRES to undergo an inchworm-walk translocation.	DISCUSS
62	67	tRNAs	chemical	Like in the 2tRNA•mRNA translocating complex in which the two tRNAs move independently of each other, the PKI domain moves relative to the 5´-domain, causing the IRES to undergo an inchworm-walk translocation.	DISCUSS
106	109	PKI	structure_element	Like in the 2tRNA•mRNA translocating complex in which the two tRNAs move independently of each other, the PKI domain moves relative to the 5´-domain, causing the IRES to undergo an inchworm-walk translocation.	DISCUSS
139	148	5´-domain	structure_element	Like in the 2tRNA•mRNA translocating complex in which the two tRNAs move independently of each other, the PKI domain moves relative to the 5´-domain, causing the IRES to undergo an inchworm-walk translocation.	DISCUSS
162	166	IRES	site	Like in the 2tRNA•mRNA translocating complex in which the two tRNAs move independently of each other, the PKI domain moves relative to the 5´-domain, causing the IRES to undergo an inchworm-walk translocation.	DISCUSS
181	189	inchworm	protein_state	Like in the 2tRNA•mRNA translocating complex in which the two tRNAs move independently of each other, the PKI domain moves relative to the 5´-domain, causing the IRES to undergo an inchworm-walk translocation.	DISCUSS
42	46	IRES	site	A large structural difference between the IRES and the 2tRNA•mRNA complex exists, however, in that the IRES lacks three out of six tRNA-like domains involved in tRNA translocation.	DISCUSS
55	65	2tRNA•mRNA	complex_assembly	A large structural difference between the IRES and the 2tRNA•mRNA complex exists, however, in that the IRES lacks three out of six tRNA-like domains involved in tRNA translocation.	DISCUSS
103	107	IRES	site	A large structural difference between the IRES and the 2tRNA•mRNA complex exists, however, in that the IRES lacks three out of six tRNA-like domains involved in tRNA translocation.	DISCUSS
108	113	lacks	protein_state	A large structural difference between the IRES and the 2tRNA•mRNA complex exists, however, in that the IRES lacks three out of six tRNA-like domains involved in tRNA translocation.	DISCUSS
131	148	tRNA-like domains	structure_element	A large structural difference between the IRES and the 2tRNA•mRNA complex exists, however, in that the IRES lacks three out of six tRNA-like domains involved in tRNA translocation.	DISCUSS
161	165	tRNA	chemical	A large structural difference between the IRES and the 2tRNA•mRNA complex exists, however, in that the IRES lacks three out of six tRNA-like domains involved in tRNA translocation.	DISCUSS
73	77	IRES	site	This difference likely accounts for the inefficient translocation of the IRES, which is difficult to stabilize in the post-translocation state and therefore is prone to reverse translocation.	DISCUSS
118	136	post-translocation	protein_state	This difference likely accounts for the inefficient translocation of the IRES, which is difficult to stabilize in the post-translocation state and therefore is prone to reverse translocation.	DISCUSS
39	42	TSV	species	Although structurally handicapped, the TSV IRES manages to translocate by employing ribosome dynamics that are remarkably similar to that in 2tRNA•mRNA translocation.	DISCUSS
43	47	IRES	site	Although structurally handicapped, the TSV IRES manages to translocate by employing ribosome dynamics that are remarkably similar to that in 2tRNA•mRNA translocation.	DISCUSS
84	92	ribosome	complex_assembly	Although structurally handicapped, the TSV IRES manages to translocate by employing ribosome dynamics that are remarkably similar to that in 2tRNA•mRNA translocation.	DISCUSS
141	151	2tRNA•mRNA	complex_assembly	Although structurally handicapped, the TSV IRES manages to translocate by employing ribosome dynamics that are remarkably similar to that in 2tRNA•mRNA translocation.	DISCUSS
18	26	ribosome	complex_assembly	The uniformity of ribosome dynamics underscores the idea that translocation is an inherent and structurally-optimized property of the ribosome, supported also by translocation activity in the absence of the elongation factor.	DISCUSS
134	142	ribosome	complex_assembly	The uniformity of ribosome dynamics underscores the idea that translocation is an inherent and structurally-optimized property of the ribosome, supported also by translocation activity in the absence of the elongation factor.	DISCUSS
192	202	absence of	protein_state	The uniformity of ribosome dynamics underscores the idea that translocation is an inherent and structurally-optimized property of the ribosome, supported also by translocation activity in the absence of the elongation factor.	DISCUSS
207	224	elongation factor	protein_type	The uniformity of ribosome dynamics underscores the idea that translocation is an inherent and structurally-optimized property of the ribosome, supported also by translocation activity in the absence of the elongation factor.	DISCUSS
91	94	60S	complex_assembly	This property is rendered by the relative mobility of the three major building blocks, the 60S subunit and the 40S head and body, assisted by ligand-interacting extensions including the L1 stalk and the P stalk.	DISCUSS
95	102	subunit	structure_element	This property is rendered by the relative mobility of the three major building blocks, the 60S subunit and the 40S head and body, assisted by ligand-interacting extensions including the L1 stalk and the P stalk.	DISCUSS
111	114	40S	complex_assembly	This property is rendered by the relative mobility of the three major building blocks, the 60S subunit and the 40S head and body, assisted by ligand-interacting extensions including the L1 stalk and the P stalk.	DISCUSS
115	119	head	structure_element	This property is rendered by the relative mobility of the three major building blocks, the 60S subunit and the 40S head and body, assisted by ligand-interacting extensions including the L1 stalk and the P stalk.	DISCUSS
124	128	body	structure_element	This property is rendered by the relative mobility of the three major building blocks, the 60S subunit and the 40S head and body, assisted by ligand-interacting extensions including the L1 stalk and the P stalk.	DISCUSS
142	171	ligand-interacting extensions	structure_element	This property is rendered by the relative mobility of the three major building blocks, the 60S subunit and the 40S head and body, assisted by ligand-interacting extensions including the L1 stalk and the P stalk.	DISCUSS
186	194	L1 stalk	structure_element	This property is rendered by the relative mobility of the three major building blocks, the 60S subunit and the 40S head and body, assisted by ligand-interacting extensions including the L1 stalk and the P stalk.	DISCUSS
203	210	P stalk	structure_element	This property is rendered by the relative mobility of the three major building blocks, the 60S subunit and the 40S head and body, assisted by ligand-interacting extensions including the L1 stalk and the P stalk.	DISCUSS
11	16	IRESs	site	Intergenic IRESs, in turn, represent a striking example of convergent molecular evolution.	DISCUSS
0	5	Viral	taxonomy_domain	Viral mRNAs have evolved to adopt an atypical structure to employ the inherent ribosome dynamics, to be able to hijack the host translational machinery in a simple fashion.	DISCUSS
6	11	mRNAs	chemical	Viral mRNAs have evolved to adopt an atypical structure to employ the inherent ribosome dynamics, to be able to hijack the host translational machinery in a simple fashion.	DISCUSS
46	55	structure	evidence	Viral mRNAs have evolved to adopt an atypical structure to employ the inherent ribosome dynamics, to be able to hijack the host translational machinery in a simple fashion.	DISCUSS
79	87	ribosome	complex_assembly	Viral mRNAs have evolved to adopt an atypical structure to employ the inherent ribosome dynamics, to be able to hijack the host translational machinery in a simple fashion.	DISCUSS
9	16	cryo-EM	experimental_method	Ensemble cryo-EM	DISCUSS
66	74	ribosome	complex_assembly	Our current understanding of macromolecular machines, such as the ribosome, is often limited by a gap between biophysical/biochemical studies and structural studies.	DISCUSS
110	141	biophysical/biochemical studies	experimental_method	Our current understanding of macromolecular machines, such as the ribosome, is often limited by a gap between biophysical/biochemical studies and structural studies.	DISCUSS
146	164	structural studies	experimental_method	Our current understanding of macromolecular machines, such as the ribosome, is often limited by a gap between biophysical/biochemical studies and structural studies.	DISCUSS
13	46	Förster resonance energy transfer	experimental_method	For example, Förster resonance energy transfer can provide insight into the macromolecular dynamics of an assembly at the single-molecule level but is limited to specifically labeled locations within the assembly.	DISCUSS
16	34	crystal structures	evidence	High-resolution crystal structures, on the other hand, can provide static images of an assembly, and the structural dynamics can only be inferred by comparing structures that are usually obtained in different experiments and under different, often non-native, conditions.	DISCUSS
159	169	structures	evidence	High-resolution crystal structures, on the other hand, can provide static images of an assembly, and the structural dynamics can only be inferred by comparing structures that are usually obtained in different experiments and under different, often non-native, conditions.	DISCUSS
0	7	Cryo-EM	experimental_method	Cryo-EM offers the possibility of obtaining integrated information of both structure and dynamics as demonstrated in lower-resolution studies of bacterial ribosome complexes.	DISCUSS
75	84	structure	evidence	Cryo-EM offers the possibility of obtaining integrated information of both structure and dynamics as demonstrated in lower-resolution studies of bacterial ribosome complexes.	DISCUSS
145	154	bacterial	taxonomy_domain	Cryo-EM offers the possibility of obtaining integrated information of both structure and dynamics as demonstrated in lower-resolution studies of bacterial ribosome complexes.	DISCUSS
155	163	ribosome	complex_assembly	Cryo-EM offers the possibility of obtaining integrated information of both structure and dynamics as demonstrated in lower-resolution studies of bacterial ribosome complexes.	DISCUSS
65	73	ribosome	complex_assembly	This is presumably one of the reasons why most recent studies of ribosome complexes have focused on a single high-resolution structure despite the non-uniform local resolution of the maps that likely reflects structural heterogeneity.	DISCUSS
125	134	structure	evidence	This is presumably one of the reasons why most recent studies of ribosome complexes have focused on a single high-resolution structure despite the non-uniform local resolution of the maps that likely reflects structural heterogeneity.	DISCUSS
183	187	maps	evidence	This is presumably one of the reasons why most recent studies of ribosome complexes have focused on a single high-resolution structure despite the non-uniform local resolution of the maps that likely reflects structural heterogeneity.	DISCUSS
32	40	FREALIGN	experimental_method	The computational efficiency of FREALIGN has allowed us to classify a relatively large dataset (1.1 million particles) into 15 classes (Figure 1—figure supplement 2) and obtain eight near-atomic-resolution structures from it.	DISCUSS
108	117	particles	experimental_method	The computational efficiency of FREALIGN has allowed us to classify a relatively large dataset (1.1 million particles) into 15 classes (Figure 1—figure supplement 2) and obtain eight near-atomic-resolution structures from it.	DISCUSS
206	216	structures	evidence	The computational efficiency of FREALIGN has allowed us to classify a relatively large dataset (1.1 million particles) into 15 classes (Figure 1—figure supplement 2) and obtain eight near-atomic-resolution structures from it.	DISCUSS
63	72	particles	experimental_method	The classification, which followed an initial alignment of all particles to a single reference, required about 130,000 CPU hours or about five to six full days on a 1000-CPU cluster.	DISCUSS
11	18	cryo-EM	experimental_method	Therefore, cryo-EM has the potential to become a standard tool for uncovering detailed dynamic pathways of complex macromolecular machines.	DISCUSS