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adding manually curated annotations in BioC XML files; adding annotations extracted from curated BioC XML files as JSON and tab-separated CSV; adding manually curated annotations and corresponding sentences extracted from BioC XML as IOB formated input for training

BioC_XML/4781976_v0.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE collection SYSTEM "BioC.dtd">
+<collection>
+  <source>PMC</source>
+  <date>20201222</date>
+  <key>pmc.key</key>
+  <document>
+    <id>4781976</id>
+    <infon key="license">CC BY</infon>
+    <infon key="tt_curatable">no</infon>
+    <infon key="tt_version">0</infon>
+    <infon key="tt_round">0</infon>
+    <passage>
+      <infon key="article-id_doi">10.1016/j.dib.2016.02.042</infon>
+      <infon key="article-id_pmc">4781976</infon>
+      <infon key="article-id_pmid">26977434</infon>
+      <infon key="article-id_publisher-id">S2352-3409(16)30064-6</infon>
+      <infon key="fpage">344</infon>
+      <infon key="kwd">Tom1, GAT domain, Tollip, Ubiquitin, nuclear magnetic resonance</infon>
+      <infon key="license">This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).</infon>
+      <infon key="lpage">348</infon>
+      <infon key="name_0">surname:Xiao;given-names:Shuyan</infon>
+      <infon key="name_1">surname:Ellena;given-names:Jeffrey F.</infon>
+      <infon key="name_2">surname:Armstrong;given-names:Geoffrey S.</infon>
+      <infon key="name_3">surname:Capelluto;given-names:Daniel G.S.</infon>
+      <infon key="section_type">TITLE</infon>
+      <infon key="title">Keywords</infon>
+      <infon key="type">front</infon>
+      <infon key="volume">7</infon>
+      <infon key="year">2016</infon>
+      <offset>0</offset>
+      <text>Structure of the GAT domain of the endosomal adapter protein Tom1</text>
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+        <infon key="identifier">DUMMY:</infon>
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+        <text>Structure</text>
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+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:58Z</infon>
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+        <text>GAT</text>
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+        <infon key="identifier">MESH:</infon>
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+        <text>adapter protein</text>
+      </annotation>
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+        <text>Tom1</text>
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+      <infon key="section_type">ABSTRACT</infon>
+      <infon key="type">abstract</infon>
+      <offset>66</offset>
+      <text>Cellular homeostasis requires correct delivery of cell-surface receptor proteins (cargo) to their target subcellular compartments. The adapter proteins Tom1 and Tollip are involved in sorting of ubiquitinated cargo in endosomal compartments. Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD). In this data article, we report the solution NMR-derived structure of the Tom1 GAT domain. The estimated protein structure exhibits a bundle of three helical elements. We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states.</text>
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+        <text>cell-surface receptor</text>
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+        <text>Tom1</text>
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+        <text>ubiquitinated</text>
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+        <text>Tom1-binding domain</text>
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+        <infon key="identifier">SO:</infon>
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+        <text>TBD</text>
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+        <text>solution NMR</text>
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+        <text>structure</text>
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+        <text>Tom1</text>
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+        <infon key="identifier">MESH:</infon>
+        <location offset="612" length="7"/>
+        <text>compare</text>
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+        <text>Tom1</text>
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+        <text>GAT</text>
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+        <text>structure</text>
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+        <text>structures</text>
+      </annotation>
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+        <text>Tollip</text>
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+        <text>TBD-</text>
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+        <text>ubiquitin-bound</text>
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+    <passage>
+      <infon key="section_type">TABLE</infon>
+      <infon key="type">title_1</infon>
+      <offset>730</offset>
+      <text>Specifications table</text>
+    </passage>
+    <passage>
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+      <infon key="section_type">TABLE</infon>
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+      <infon key="xml">&lt;?xml version="1.0" encoding="UTF-8"?&gt;
+&lt;table frame="hsides" rules="groups"&gt;&lt;tbody&gt;&lt;tr&gt;&lt;td&gt;Subject area&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Biology&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;More specific subject area&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Structural biology&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Type of data&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Table, text file, graph, figures&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;How data was acquired&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Circular dichroism and NMR. NMR data was recorded using a Bruker 800 MHz&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Data format&lt;/td&gt;&lt;td&gt;&lt;italic&gt;PDB format text file. Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Experimental factors&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Recombinant human Tom1 GAT domain was purified to homogeneity before use&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Experimental features&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Solution structure of Tom1 GAT was determined from NMR chemical shift data&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Data source location&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Virginia and Colorado, United States.&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Data accessibility&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Data is available within this article. Tom1 GAT structural data is publicly available in the RCSB Protein Data Bank (http://www.rscb.org/) under the accession number PDB: 2n9d&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;/tbody&gt;&lt;/table&gt;
+</infon>
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+      <text>Table	 	</text>
+    </passage>
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+      <infon key="id">t0010</infon>
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+&lt;table frame="hsides" rules="groups"&gt;&lt;tbody&gt;&lt;tr&gt;&lt;td&gt;Subject area&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Biology&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;More specific subject area&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Structural biology&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Type of data&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Table, text file, graph, figures&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;How data was acquired&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Circular dichroism and NMR. NMR data was recorded using a Bruker 800 MHz&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Data format&lt;/td&gt;&lt;td&gt;&lt;italic&gt;PDB format text file. Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Experimental factors&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Recombinant human Tom1 GAT domain was purified to homogeneity before use&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Experimental features&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Solution structure of Tom1 GAT was determined from NMR chemical shift data&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Data source location&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Virginia and Colorado, United States.&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Data accessibility&lt;/td&gt;&lt;td&gt;&lt;italic&gt;Data is available within this article. Tom1 GAT structural data is publicly available in the RCSB Protein Data Bank (http://www.rscb.org/) under the accession number PDB: 2n9d&lt;/italic&gt;&lt;/td&gt;&lt;/tr&gt;&lt;/tbody&gt;&lt;/table&gt;
+</infon>
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+      <text>Subject area	Biology	 	More specific subject area	Structural biology	 	Type of data	Table, text file, graph, figures	 	How data was acquired	Circular dichroism and NMR. NMR data was recorded using a Bruker 800 MHz	 	Data format	PDB format text file. Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States.	 	Data accessibility	Data is available within this article. Tom1 GAT structural data is publicly available in the RCSB Protein Data Bank (http://www.rscb.org/) under the accession number PDB: 2n9d	 	</text>
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+        <text>Tom1</text>
+      </annotation>
+      <annotation id="38">
+        <infon key="score">0.5058204</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:58Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="1152" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="39">
+        <infon key="score">0.99844825</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:00:14Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="1226" length="18"/>
+        <text>Solution structure</text>
+      </annotation>
+      <annotation id="40">
+        <infon key="score">0.99984014</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="1248" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="41">
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+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:58Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="1253" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="42">
+        <infon key="score">0.9996598</infon>
+        <infon key="type">experimental_method</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:59:32Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="1277" length="3"/>
+        <text>NMR</text>
+      </annotation>
+      <annotation id="238">
+        <infon key="type">evidence</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:00:28Z</infon>
+        <location offset="1281" length="14"/>
+        <text>chemical shift</text>
+      </annotation>
+      <annotation id="193">
+        <infon key="type">protein</infon>
+        <infon key="identifier">PR:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <location offset="1422" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="212">
+        <infon key="type">structure_element</infon>
+        <infon key="identifier">SO:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:58Z</infon>
+        <location offset="1427" length="3"/>
+        <text>GAT</text>
+      </annotation>
+    </passage>
+    <passage>
+      <infon key="section_type">TABLE</infon>
+      <infon key="type">title_1</infon>
+      <offset>1563</offset>
+      <text>Value of the data</text>
+    </passage>
+    <passage>
+      <infon key="section_type">TABLE</infon>
+      <infon key="type">paragraph</infon>
+      <offset>1581</offset>
+      <text>The Tom1 GAT domain solution structure will provide additional tools for modulating its biological function.</text>
+      <annotation id="45">
+        <infon key="score">0.99983656</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="1585" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="213">
+        <infon key="type">structure_element</infon>
+        <infon key="identifier">SO:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:58Z</infon>
+        <location offset="1590" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="47">
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+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:00:14Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="1601" length="18"/>
+        <text>solution structure</text>
+      </annotation>
+    </passage>
+    <passage>
+      <infon key="section_type">TABLE</infon>
+      <infon key="type">paragraph</infon>
+      <offset>1690</offset>
+      <text>Tom1 GAT can adopt distinct conformations upon ligand binding.</text>
+      <annotation id="48">
+        <infon key="score">0.999843</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="1690" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="49">
+        <infon key="score">0.9992766</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:58Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="1695" length="3"/>
+        <text>GAT</text>
+      </annotation>
+    </passage>
+    <passage>
+      <infon key="section_type">TABLE</infon>
+      <infon key="type">paragraph</infon>
+      <offset>1753</offset>
+      <text>A conformational response of the Tom1 GAT domain upon Tollip TBD binding can serve as an example to explain mutually exclusive ligand binding events.</text>
+      <annotation id="50">
+        <infon key="score">0.99981683</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="1786" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="214">
+        <infon key="type">structure_element</infon>
+        <infon key="identifier">SO:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:58Z</infon>
+        <location offset="1791" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="52">
+        <infon key="score">0.9990669</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:16Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="1807" length="6"/>
+        <text>Tollip</text>
+      </annotation>
+      <annotation id="53">
+        <infon key="score">0.99973947</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:36Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="1814" length="3"/>
+        <text>TBD</text>
+      </annotation>
+    </passage>
+    <passage>
+      <infon key="section_type">TABLE</infon>
+      <infon key="type">title_1</infon>
+      <offset>1903</offset>
+      <text>Data</text>
+    </passage>
+    <passage>
+      <infon key="section_type">TABLE</infon>
+      <infon key="type">paragraph</infon>
+      <offset>1908</offset>
+      <text>Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions. The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B).</text>
+      <annotation id="54">
+        <infon key="score">0.99765813</infon>
+        <infon key="type">experimental_method</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:25Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="1924" length="25"/>
+        <text>far-UV circular dichroism</text>
+      </annotation>
+      <annotation id="55">
+        <infon key="score">0.97389156</infon>
+        <infon key="type">experimental_method</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:22Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="1951" length="2"/>
+        <text>CD</text>
+      </annotation>
+      <annotation id="56">
+        <infon key="score">0.9930906</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:19Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="1955" length="8"/>
+        <text>spectrum</text>
+      </annotation>
+      <annotation id="57">
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+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:06:22Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="1971" length="5"/>
+        <text>Tom 1</text>
+      </annotation>
+      <annotation id="215">
+        <infon key="type">structure_element</infon>
+        <infon key="identifier">SO:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:58Z</infon>
+        <location offset="1977" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="59">
+        <infon key="score">0.999609</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:58Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="2012" length="7"/>
+        <text>α-helix</text>
+      </annotation>
+      <annotation id="60">
+        <infon key="score">0.9994879</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:59Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="2024" length="8"/>
+        <text>β-strand</text>
+      </annotation>
+      <annotation id="61">
+        <infon key="score">0.99985206</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="2080" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="62">
+        <infon key="score">0.7947963</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:58Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="2085" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="63">
+        <infon key="score">0.9988989</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:06:41Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="2089" length="21"/>
+        <text>structural restraints</text>
+      </annotation>
+      <annotation id="64">
+        <infon key="score">0.9295965</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:06:45Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="2131" length="10"/>
+        <text>structures</text>
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+      <annotation id="65">
+        <infon key="score">0.9993277</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:33Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="2161" length="26"/>
+        <text>root mean square deviation</text>
+      </annotation>
+      <annotation id="66">
+        <infon key="score">0.9996222</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:36Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="2189" length="4"/>
+        <text>RMSD</text>
+      </annotation>
+      <annotation id="67">
+        <infon key="score">0.9990892</infon>
+        <infon key="type">residue_range</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:42Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="2319" length="9"/>
+        <text>Q216-E240</text>
+      </annotation>
+      <annotation id="68">
+        <infon key="score">0.9997021</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:49Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="2330" length="9"/>
+        <text>α-helix 1</text>
+      </annotation>
+      <annotation id="69">
+        <infon key="score">0.9991074</infon>
+        <infon key="type">residue_range</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:44Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="2342" length="9"/>
+        <text>P248-Q274</text>
+      </annotation>
+      <annotation id="70">
+        <infon key="score">0.9997027</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:51Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="2353" length="9"/>
+        <text>α-helix 2</text>
+      </annotation>
+      <annotation id="71">
+        <infon key="score">0.99909496</infon>
+        <infon key="type">residue_range</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:46Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="2369" length="9"/>
+        <text>E278-T306</text>
+      </annotation>
+      <annotation id="72">
+        <infon key="score">0.99970627</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:53Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="2380" length="9"/>
+        <text>α-helix 3</text>
+      </annotation>
+      <annotation id="73">
+        <infon key="score">0.99831545</infon>
+        <infon key="type">chemical</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:07:05Z</infon>
+        <infon key="identifier">CHEBI:</infon>
+        <location offset="2399" length="9"/>
+        <text>ubiquitin</text>
+      </annotation>
+      <annotation id="74">
+        <infon key="score">0.99984026</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="2466" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="75">
+        <infon key="score">0.99932325</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:58Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="2471" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="76">
+        <infon key="score">0.9996645</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:01:56Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="2475" length="17"/>
+        <text>α-helices 1 and 2</text>
+      </annotation>
+      <annotation id="77">
+        <infon key="score">0.9998336</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:16Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="2504" length="6"/>
+        <text>Tollip</text>
+      </annotation>
+      <annotation id="78">
+        <infon key="score">0.9960354</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:36Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="2511" length="3"/>
+        <text>TBD</text>
+      </annotation>
+    </passage>
+    <passage>
+      <infon key="section_type">METHODS</infon>
+      <infon key="type">title_1</infon>
+      <offset>2559</offset>
+      <text>Experimental design, materials, and methods</text>
+    </passage>
+    <passage>
+      <infon key="section_type">METHODS</infon>
+      <infon key="type">title_2</infon>
+      <offset>2603</offset>
+      <text>Protein expression and purification</text>
+    </passage>
+    <passage>
+      <infon key="section_type">METHODS</infon>
+      <infon key="type">paragraph</infon>
+      <offset>2639</offset>
+      <text>Human Tom1 GAT (residues 215–309) cDNA was cloned into both pGEX6P1 and pET28a vectors, and expressed as GST-tagged and His-tagged fusion proteins, respectively, using Escherichia coli [Rosetta (DE3) strain]. The 13C, 15N-labeled Tom1 GAT domain was expressed and purified as described previously.</text>
+    </passage>
+    <passage>
+      <infon key="section_type">METHODS</infon>
+      <infon key="type">title_2</infon>
+      <offset>2939</offset>
+      <text>Circular dichroism</text>
+    </passage>
+    <passage>
+      <infon key="section_type">METHODS</infon>
+      <infon key="type">paragraph</infon>
+      <offset>2958</offset>
+      <text>Far-UV CD spectra of the His-Tom1 GAT domain were collected on a Jasco J-815 spectropolarimeter using a 1 mm path length quartz cell at room temperature. The protein (10 μM) was solubilized in 5 mM Tris–HCl (pH 7) and 100 mM KF. Spectra were obtained from five accumulated scans from 190 to 260 nm using a bandwidth of 1 nm and a response time of 1 s at a scan speed of 20 nm/min. Buffer backgrounds were employed to subtract the protein spectra. Data was processed using the Dichroweb server and the CONTIN algorithm (http://dichroweb.cryst.bbk.ac.uk/html/home.shtml).</text>
+    </passage>
+    <passage>
+      <infon key="section_type">METHODS</infon>
+      <infon key="type">title_2</infon>
+      <offset>3539</offset>
+      <text>NMR structure determination</text>
+    </passage>
+    <passage>
+      <infon key="section_type">METHODS</infon>
+      <infon key="type">paragraph</infon>
+      <offset>3567</offset>
+      <text>NMR experiments were performed using 1 mM 13C, 15N-labeled Tom1 GAT domain in a buffer containing 20 mM d11-TrisHCl (pH 7), 50 mM KCl, 1 mM d18-DTT, and 1 mM NaN3. NMR spectra were recorded at 25 °C on a Bruker 800-MHz spectrometer (University of Virginia). The individual structure of Tom1 GAT was generated using CS-Rosetta (https://csrosetta.bmrb.wisc.edu/csrosetta). Chemical shift information (BMRB #26574) was used to obtain the structure calculation. The Rosetta calculations yielded 3000 structures of Tom1 GAT. From these, ten structures were selected based on their score and RMSDs, and converted to Protein Data Bank (PDB) format. NMR structural statistics for the ten lowest energy conformers of Tom1 GAT was generated using the Protein Structure Validation Suite. By using MolProbity, the Ramachandran analysis of the ten superimposed Tom1 GAT structures identified that 100% of the residues were in the most favored regions and there were no Ramachandran outliers in the allowed and disallowed regions. Protein structure images were obtained using PyMol (http://www.pymol.org). The structures of the ubiquitin- and Tollip TBD-bound states of the Tom1 GAT domain were obtained from data reported in Refs. and.</text>
+    </passage>
+    <passage>
+      <infon key="section_type">REF</infon>
+      <infon key="type">title</infon>
+      <offset>4797</offset>
+      <text>References</text>
+    </passage>
+    <passage>
+      <infon key="fpage">1910</infon>
+      <infon key="lpage">1920</infon>
+      <infon key="name_0">surname:Xiao;given-names:S.</infon>
+      <infon key="name_1">surname:Brannon;given-names:M.K.</infon>
+      <infon key="name_2">surname:Zhao;given-names:X.</infon>
+      <infon key="name_3">surname:Fread;given-names:K.I.</infon>
+      <infon key="name_4">surname:Ellena;given-names:J.F.</infon>
+      <infon key="name_5">surname:Bushweller;given-names:J.H.</infon>
+      <infon key="name_6">surname:Finkielstein;given-names:C.V.</infon>
+      <infon key="name_7">surname:Armstrong;given-names:G.S.</infon>
+      <infon key="name_8">surname:Capelluto;given-names:D.G.</infon>
+      <infon key="section_type">REF</infon>
+      <infon key="source">Structure</infon>
+      <infon key="type">ref</infon>
+      <infon key="volume">23</infon>
+      <infon key="year">2015</infon>
+      <offset>4808</offset>
+      <text>Tom1 modulates binding of Tollip to phosphatidylinositol 3-phosphate via a coupled folding and binding mechanism</text>
+    </passage>
+    <passage>
+      <infon key="fpage">5385</infon>
+      <infon key="lpage">5391</infon>
+      <infon key="name_0">surname:Akutsu;given-names:M.</infon>
+      <infon key="name_1">surname:Kawasaki;given-names:M.</infon>
+      <infon key="name_2">surname:Katoh;given-names:Y.</infon>
+      <infon key="name_3">surname:Shiba;given-names:T.</infon>
+      <infon key="name_4">surname:Yamaguchi;given-names:Y.</infon>
+      <infon key="name_5">surname:Kato;given-names:R.</infon>
+      <infon key="name_6">surname:Kato;given-names:K.</infon>
+      <infon key="name_7">surname:Nakayama;given-names:K.</infon>
+      <infon key="name_8">surname:Wakatsuki;given-names:S.</infon>
+      <infon key="pub-id_pmid">16199040</infon>
+      <infon key="section_type">REF</infon>
+      <infon key="source">FEBS Lett.</infon>
+      <infon key="type">ref</infon>
+      <infon key="volume">579</infon>
+      <infon key="year">2005</infon>
+      <offset>4921</offset>
+      <text>Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain</text>
+    </passage>
+    <passage>
+      <infon key="section_type">SUPPL</infon>
+      <infon key="type">title_1</infon>
+      <offset>4996</offset>
+      <text>Supplementary material</text>
+    </passage>
+    <passage>
+      <infon key="section_type">SUPPL</infon>
+      <infon key="type">footnote</infon>
+      <offset>5019</offset>
+      <text>Supplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2016.02.042.</text>
+    </passage>
+    <passage>
+      <infon key="file">gr1.jpg</infon>
+      <infon key="id">f0005</infon>
+      <infon key="section_type">FIG</infon>
+      <infon key="type">fig_caption</infon>
+      <offset>5136</offset>
+      <text>Representative far-UV CD spectrum of the His-Tom1 GAT domain.</text>
+      <annotation id="151">
+        <infon key="score">0.99858</infon>
+        <infon key="type">experimental_method</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:03:56Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="5151" length="9"/>
+        <text>far-UV CD</text>
+      </annotation>
+      <annotation id="152">
+        <infon key="score">0.71714723</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:06:50Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="5161" length="8"/>
+        <text>spectrum</text>
+      </annotation>
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+        <infon key="score">0.8865229</infon>
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+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:04:25Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="5177" length="4"/>
+        <text>His-</text>
+      </annotation>
+      <annotation id="154">
+        <infon key="score">0.9922563</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="5181" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="225">
+        <infon key="type">structure_element</infon>
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+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:59Z</infon>
+        <location offset="5186" length="3"/>
+        <text>GAT</text>
+      </annotation>
+    </passage>
+    <passage>
+      <infon key="file">gr1.jpg</infon>
+      <infon key="id">f0005</infon>
+      <infon key="section_type">FIG</infon>
+      <infon key="type">fig</infon>
+      <offset>5198</offset>
+      <text>Fig. 1.</text>
+    </passage>
+    <passage>
+      <infon key="file">gr2.jpg</infon>
+      <infon key="id">f0010</infon>
+      <infon key="section_type">FIG</infon>
+      <infon key="type">fig_caption</infon>
+      <offset>5206</offset>
+      <text>(A) Stereo view displaying the best-fit backbone superposition of the refined structures for the Tom1 GAT domain. Helices are shown in orange, whereas loops are colored in green. (B) Ribbon illustration of the Tom1 GAT domain.</text>
+      <annotation id="156">
+        <infon key="score">0.9992467</infon>
+        <infon key="type">experimental_method</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:04:41Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="5246" length="22"/>
+        <text>backbone superposition</text>
+      </annotation>
+      <annotation id="157">
+        <infon key="score">0.9941738</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:06:54Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="5284" length="10"/>
+        <text>structures</text>
+      </annotation>
+      <annotation id="158">
+        <infon key="score">0.9998486</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="5303" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="226">
+        <infon key="type">structure_element</infon>
+        <infon key="identifier">SO:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:59Z</infon>
+        <location offset="5308" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="160">
+        <infon key="score">0.99984694</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="5416" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="227">
+        <infon key="type">structure_element</infon>
+        <infon key="identifier">SO:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:59Z</infon>
+        <location offset="5421" length="3"/>
+        <text>GAT</text>
+      </annotation>
+    </passage>
+    <passage>
+      <infon key="file">gr2.jpg</infon>
+      <infon key="id">f0010</infon>
+      <infon key="section_type">FIG</infon>
+      <infon key="type">fig</infon>
+      <offset>5433</offset>
+      <text>Fig. 2.</text>
+    </passage>
+    <passage>
+      <infon key="file">gr3.jpg</infon>
+      <infon key="id">f0015</infon>
+      <infon key="section_type">FIG</infon>
+      <infon key="type">fig_caption</infon>
+      <offset>5441</offset>
+      <text>(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).</text>
+      <annotation id="162">
+        <infon key="score">0.9534955</infon>
+        <infon key="type">experimental_method</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:05:10Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="5462" length="23"/>
+        <text>superimposed structures</text>
+      </annotation>
+      <annotation id="163">
+        <infon key="score">0.99984646</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="5493" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="228">
+        <infon key="type">structure_element</infon>
+        <infon key="identifier">SO:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:59Z</infon>
+        <location offset="5498" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="165">
+        <infon key="score">0.99965954</infon>
+        <infon key="type">protein_state</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:05:18Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="5516" length="4"/>
+        <text>free</text>
+      </annotation>
+      <annotation id="166">
+        <infon key="score">0.9996728</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:16Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="5551" length="6"/>
+        <text>Tollip</text>
+      </annotation>
+      <annotation id="167">
+        <infon key="score">0.99953216</infon>
+        <infon key="type">protein_state</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:05:15Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="5558" length="9"/>
+        <text>TBD-bound</text>
+      </annotation>
+      <annotation id="168">
+        <infon key="score">0.9632287</infon>
+        <infon key="type">experimental_method</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:05:12Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="5602" length="23"/>
+        <text>superimposed structures</text>
+      </annotation>
+      <annotation id="169">
+        <infon key="score">0.9998419</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="5633" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="229">
+        <infon key="type">structure_element</infon>
+        <infon key="identifier">SO:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:59Z</infon>
+        <location offset="5638" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="171">
+        <infon key="score">0.9995443</infon>
+        <infon key="type">protein_state</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:05:16Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="5673" length="8"/>
+        <text>Ub-bound</text>
+      </annotation>
+    </passage>
+    <passage>
+      <infon key="file">gr3.jpg</infon>
+      <infon key="id">f0015</infon>
+      <infon key="section_type">FIG</infon>
+      <infon key="type">fig</infon>
+      <offset>5697</offset>
+      <text>Fig. 3.</text>
+    </passage>
+    <passage>
+      <infon key="file">t0005.xml</infon>
+      <infon key="id">t0005</infon>
+      <infon key="section_type">TABLE</infon>
+      <infon key="type">table_caption</infon>
+      <offset>5705</offset>
+      <text>NMR and refinement statistics for the Tom1 GAT domain. NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS.</text>
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+        <infon key="score">0.99963295</infon>
+        <infon key="type">experimental_method</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:59:32Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="5705" length="3"/>
+        <text>NMR</text>
+      </annotation>
+      <annotation id="173">
+        <infon key="score">0.9961254</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:05:29Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="5713" length="21"/>
+        <text>refinement statistics</text>
+      </annotation>
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+        <infon key="score">0.9998447</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="5743" length="4"/>
+        <text>Tom1</text>
+      </annotation>
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+        <infon key="type">structure_element</infon>
+        <infon key="identifier">SO:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:59Z</infon>
+        <location offset="5748" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="176">
+        <infon key="score">0.999608</infon>
+        <infon key="type">experimental_method</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:59:32Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="5760" length="3"/>
+        <text>NMR</text>
+      </annotation>
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+        <infon key="score">0.9994303</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:05:33Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="5764" length="21"/>
+        <text>structural statistics</text>
+      </annotation>
+      <annotation id="178">
+        <infon key="score">0.99985063</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="5818" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="179">
+        <infon key="score">0.9986708</infon>
+        <infon key="type">structure_element</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:59Z</infon>
+        <infon key="identifier">SO:</infon>
+        <location offset="5823" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="180">
+        <infon key="score">0.9996277</infon>
+        <infon key="type">experimental_method</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:05:31Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="5833" length="4"/>
+        <text>PSVS</text>
+      </annotation>
+    </passage>
+    <passage>
+      <infon key="file">t0005.xml</infon>
+      <infon key="id">t0005</infon>
+      <infon key="section_type">TABLE</infon>
+      <infon key="type">table</infon>
+      <infon key="xml">&lt;?xml version="1.0" encoding="UTF-8"?&gt;
+&lt;table frame="hsides" rules="groups"&gt;&lt;thead&gt;&lt;tr&gt;&lt;th/&gt;&lt;th&gt;&lt;bold&gt;Tom1 GAT&lt;/bold&gt;&lt;/th&gt;&lt;/tr&gt;&lt;/thead&gt;&lt;tbody&gt;&lt;tr&gt;&lt;td&gt;&lt;bold&gt;NMR distance and dihedral constraints&lt;/bold&gt;&lt;/td&gt;&lt;td/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Dihedral angle restraints total&lt;/td&gt;&lt;td&gt;178&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;&lt;italic&gt; ϕ&lt;/italic&gt;&lt;/td&gt;&lt;td&gt;89&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;&lt;italic&gt; ψ&lt;/italic&gt;&lt;/td&gt;&lt;td&gt;89&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;&lt;bold&gt;Structure statistics&lt;/bold&gt;&lt;/td&gt;&lt;td/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Dihedral angle constraints (deg)&lt;/td&gt;&lt;td&gt;8.8±0.2&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Max. dihedral angle violation (deg)&lt;/td&gt;&lt;td&gt;111±3&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Deviations from idealized geometry&lt;/td&gt;&lt;td/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Bond lengths (Å)&lt;/td&gt;&lt;td&gt;0.011&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Bond angles (deg)&lt;/td&gt;&lt;td&gt;0.7&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Average pairwise r.m.s. deviation (Å)&lt;xref rid="tbl1fna" ref-type="table-fn"&gt;a&lt;/xref&gt;&lt;/td&gt;&lt;td/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Protein&lt;/td&gt;&lt;td/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Heavy&lt;/td&gt;&lt;td&gt;1.3&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Backbone&lt;/td&gt;&lt;td&gt;0.9&lt;/td&gt;&lt;/tr&gt;&lt;/tbody&gt;&lt;/table&gt;
+</infon>
+      <offset>5839</offset>
+      <text>Table 1.	 	</text>
+    </passage>
+    <passage>
+      <infon key="file">t0005.xml</infon>
+      <infon key="id">t0005</infon>
+      <infon key="section_type">TABLE</infon>
+      <infon key="type">table</infon>
+      <infon key="xml">&lt;?xml version="1.0" encoding="UTF-8"?&gt;
+&lt;table frame="hsides" rules="groups"&gt;&lt;thead&gt;&lt;tr&gt;&lt;th/&gt;&lt;th&gt;&lt;bold&gt;Tom1 GAT&lt;/bold&gt;&lt;/th&gt;&lt;/tr&gt;&lt;/thead&gt;&lt;tbody&gt;&lt;tr&gt;&lt;td&gt;&lt;bold&gt;NMR distance and dihedral constraints&lt;/bold&gt;&lt;/td&gt;&lt;td/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Dihedral angle restraints total&lt;/td&gt;&lt;td&gt;178&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;&lt;italic&gt; ϕ&lt;/italic&gt;&lt;/td&gt;&lt;td&gt;89&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;&lt;italic&gt; ψ&lt;/italic&gt;&lt;/td&gt;&lt;td&gt;89&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;&lt;bold&gt;Structure statistics&lt;/bold&gt;&lt;/td&gt;&lt;td/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Dihedral angle constraints (deg)&lt;/td&gt;&lt;td&gt;8.8±0.2&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Max. dihedral angle violation (deg)&lt;/td&gt;&lt;td&gt;111±3&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Deviations from idealized geometry&lt;/td&gt;&lt;td/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Bond lengths (Å)&lt;/td&gt;&lt;td&gt;0.011&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Bond angles (deg)&lt;/td&gt;&lt;td&gt;0.7&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;Average pairwise r.m.s. deviation (Å)&lt;xref rid="tbl1fna" ref-type="table-fn"&gt;a&lt;/xref&gt;&lt;/td&gt;&lt;td/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Protein&lt;/td&gt;&lt;td/&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Heavy&lt;/td&gt;&lt;td&gt;1.3&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt; Backbone&lt;/td&gt;&lt;td&gt;0.9&lt;/td&gt;&lt;/tr&gt;&lt;/tbody&gt;&lt;/table&gt;
+</infon>
+      <offset>5851</offset>
+      <text>	Tom1 GAT	 	NMR distance and dihedral constraints		 	 Dihedral angle restraints total	178	 	 ϕ	89	 	 ψ	89	 	Structure statistics		 	 Dihedral angle constraints (deg)	8.8±0.2	 	 Max. dihedral angle violation (deg)	111±3	 	Deviations from idealized geometry		 	 Bond lengths (Å)	0.011	 	 Bond angles (deg)	0.7	 	Average pairwise r.m.s. deviation (Å)a		 	 Protein		 	 Heavy	1.3	 	 Backbone	0.9	 	</text>
+    </passage>
+    <passage>
+      <infon key="file">t0005.xml</infon>
+      <infon key="id">t0005</infon>
+      <infon key="section_type">TABLE</infon>
+      <infon key="type">table_footnote</infon>
+      <offset>6261</offset>
+      <text>Pairwise backbone and heavy-atom r.m.s. deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures.</text>
+      <annotation id="187">
+        <infon key="score">0.9994108</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:05:50Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="6294" length="17"/>
+        <text>r.m.s. deviations</text>
+      </annotation>
+      <annotation id="188">
+        <infon key="score">0.99964523</infon>
+        <infon key="type">experimental_method</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:05:52Z</infon>
+        <infon key="identifier">MESH:</infon>
+        <location offset="6329" length="13"/>
+        <text>superimposing</text>
+      </annotation>
+      <annotation id="189">
+        <infon key="score">0.9990513</infon>
+        <infon key="type">residue_range</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:05:56Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="6352" length="7"/>
+        <text>215–309</text>
+      </annotation>
+      <annotation id="190">
+        <infon key="score">0.99986255</infon>
+        <infon key="type">protein</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:12Z</infon>
+        <infon key="identifier">PR:</infon>
+        <location offset="6363" length="4"/>
+        <text>Tom1</text>
+      </annotation>
+      <annotation id="232">
+        <infon key="type">structure_element</infon>
+        <infon key="identifier">SO:</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T14:57:59Z</infon>
+        <location offset="6368" length="3"/>
+        <text>GAT</text>
+      </annotation>
+      <annotation id="191">
+        <infon key="score">0.9991259</infon>
+        <infon key="type">evidence</infon>
+        <infon key="annotator">cleaner0</infon>
+        <infon key="updated_at">2023-07-20T15:06:59Z</infon>
+        <infon key="identifier">DUMMY:</infon>
+        <location offset="6403" length="10"/>
+        <text>structures</text>
+      </annotation>
+    </passage>
+  </document>
+</collection>

annotation_CSV/PMC4781976.csv

@@ -0,0 +1,114 @@
+anno_start	anno_end	anno_text	entity_type	sentence	section
+0	9	Structure	evidence	Structure of the GAT domain of the endosomal adapter protein Tom1	TITLE
+17	20	GAT	structure_element	Structure of the GAT domain of the endosomal adapter protein Tom1	TITLE
+45	60	adapter protein	protein_type	Structure of the GAT domain of the endosomal adapter protein Tom1	TITLE
+61	65	Tom1	protein	Structure of the GAT domain of the endosomal adapter protein Tom1	TITLE
+50	71	cell-surface receptor	protein_type	Cellular homeostasis requires correct delivery of cell-surface receptor proteins (cargo) to their target subcellular compartments.	ABSTRACT
+4	20	adapter proteins	protein_type	The adapter proteins Tom1 and Tollip are involved in sorting of ubiquitinated cargo in endosomal compartments.	ABSTRACT
+21	25	Tom1	protein	The adapter proteins Tom1 and Tollip are involved in sorting of ubiquitinated cargo in endosomal compartments.	ABSTRACT
+30	36	Tollip	protein	The adapter proteins Tom1 and Tollip are involved in sorting of ubiquitinated cargo in endosomal compartments.	ABSTRACT
+64	77	ubiquitinated	ptm	The adapter proteins Tom1 and Tollip are involved in sorting of ubiquitinated cargo in endosomal compartments.	ABSTRACT
+15	19	Tom1	protein	Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD).	ABSTRACT
+69	72	GAT	structure_element	Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD).	ABSTRACT
+97	103	Tollip	protein	Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD).	ABSTRACT
+106	125	Tom1-binding domain	structure_element	Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD).	ABSTRACT
+127	130	TBD	structure_element	Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD).	ABSTRACT
+36	48	solution NMR	experimental_method	In this data article, we report the solution NMR-derived structure of the Tom1 GAT domain.	ABSTRACT
+57	66	structure	evidence	In this data article, we report the solution NMR-derived structure of the Tom1 GAT domain.	ABSTRACT
+74	78	Tom1	protein	In this data article, we report the solution NMR-derived structure of the Tom1 GAT domain.	ABSTRACT
+79	82	GAT	structure_element	In this data article, we report the solution NMR-derived structure of the Tom1 GAT domain.	ABSTRACT
+22	31	structure	evidence	The estimated protein structure exhibits a bundle of three helical elements.	ABSTRACT
+3	10	compare	experimental_method	We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states.	ABSTRACT
+15	19	Tom1	protein	We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states.	ABSTRACT
+20	23	GAT	structure_element	We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states.	ABSTRACT
+24	33	structure	evidence	We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states.	ABSTRACT
+45	55	structures	evidence	We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states.	ABSTRACT
+77	83	Tollip	protein	We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states.	ABSTRACT
+84	88	TBD-	protein_state	We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states.	ABSTRACT
+93	108	ubiquitin-bound	protein_state	We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states.	ABSTRACT
+141	159	Circular dichroism	experimental_method	"Subject area	Biology	 	More specific subject area	Structural biology	 	Type of data	Table, text file, graph, figures	 	How data was acquired	Circular dichroism and NMR."	TABLE
+164	167	NMR	experimental_method	"Subject area	Biology	 	More specific subject area	Structural biology	 	Type of data	Table, text file, graph, figures	 	How data was acquired	Circular dichroism and NMR."	TABLE
+0	3	NMR	experimental_method	"NMR data was recorded using a Bruker 800 MHz	 	Data format	PDB format text file."	TABLE
+12	22	CS-Rosetta	experimental_method	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+24	59	Protein Structure Validation Server	experimental_method	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+61	65	PSVS	experimental_method	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+68	75	NMRPipe	experimental_method	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+77	84	NMRDraw	experimental_method	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+131	136	human	species	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+137	141	Tom1	protein	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+142	145	GAT	structure_element	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+216	234	Solution structure	evidence	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+238	242	Tom1	protein	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+243	246	GAT	structure_element	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+267	270	NMR	experimental_method	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+271	285	chemical shift	evidence	"Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol	 	Experimental factors	Recombinant human Tom1 GAT domain was purified to homogeneity before use	 	Experimental features	Solution structure of Tom1 GAT was determined from NMR chemical shift data	 	Data source location	Virginia and Colorado, United States."	TABLE
+5	8	GAT	structure_element	"Tom1 GAT structural data is publicly available in the RCSB Protein Data Bank (http://www.rscb.org/) under the accession number PDB: 2n9d	 	"	TABLE
+4	8	Tom1	protein	The Tom1 GAT domain solution structure will provide additional tools for modulating its biological function.	TABLE
+9	12	GAT	structure_element	The Tom1 GAT domain solution structure will provide additional tools for modulating its biological function.	TABLE
+20	38	solution structure	evidence	The Tom1 GAT domain solution structure will provide additional tools for modulating its biological function.	TABLE
+0	4	Tom1	protein	Tom1 GAT can adopt distinct conformations upon ligand binding.	TABLE
+5	8	GAT	structure_element	Tom1 GAT can adopt distinct conformations upon ligand binding.	TABLE
+33	37	Tom1	protein	A conformational response of the Tom1 GAT domain upon Tollip TBD binding can serve as an example to explain mutually exclusive ligand binding events.	TABLE
+38	41	GAT	structure_element	A conformational response of the Tom1 GAT domain upon Tollip TBD binding can serve as an example to explain mutually exclusive ligand binding events.	TABLE
+54	60	Tollip	protein	A conformational response of the Tom1 GAT domain upon Tollip TBD binding can serve as an example to explain mutually exclusive ligand binding events.	TABLE
+61	64	TBD	structure_element	A conformational response of the Tom1 GAT domain upon Tollip TBD binding can serve as an example to explain mutually exclusive ligand binding events.	TABLE
+16	41	far-UV circular dichroism	experimental_method	Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions.	TABLE
+43	45	CD	experimental_method	Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions.	TABLE
+47	55	spectrum	evidence	Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions.	TABLE
+63	68	Tom 1	protein	Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions.	TABLE
+69	72	GAT	structure_element	Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions.	TABLE
+104	111	α-helix	structure_element	Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions.	TABLE
+116	124	β-strand	structure_element	Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions.	TABLE
+4	8	Tom1	protein	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+9	12	GAT	structure_element	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+13	34	structural restraints	evidence	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+55	65	structures	evidence	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+85	111	root mean square deviation	evidence	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+113	117	RMSD	evidence	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+243	252	Q216-E240	residue_range	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+254	263	α-helix 1	structure_element	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+266	275	P248-Q274	residue_range	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+277	286	α-helix 2	structure_element	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+293	302	E278-T306	residue_range	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+304	313	α-helix 3	structure_element	The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3).	TABLE
+7	16	ubiquitin	chemical	Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B).	TABLE
+74	78	Tom1	protein	Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B).	TABLE
+79	82	GAT	structure_element	Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B).	TABLE
+83	100	α-helices 1 and 2	structure_element	Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B).	TABLE
+112	118	Tollip	protein	Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B).	TABLE
+119	122	TBD	structure_element	Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B).	TABLE
+15	24	far-UV CD	experimental_method	Representative far-UV CD spectrum of the His-Tom1 GAT domain.	FIG
+25	33	spectrum	evidence	Representative far-UV CD spectrum of the His-Tom1 GAT domain.	FIG
+41	45	His-	experimental_method	Representative far-UV CD spectrum of the His-Tom1 GAT domain.	FIG
+45	49	Tom1	protein	Representative far-UV CD spectrum of the His-Tom1 GAT domain.	FIG
+50	53	GAT	structure_element	Representative far-UV CD spectrum of the His-Tom1 GAT domain.	FIG
+40	62	backbone superposition	experimental_method	(A) Stereo view displaying the best-fit backbone superposition of the refined structures for the Tom1 GAT domain.	FIG
+78	88	structures	evidence	(A) Stereo view displaying the best-fit backbone superposition of the refined structures for the Tom1 GAT domain.	FIG
+97	101	Tom1	protein	(A) Stereo view displaying the best-fit backbone superposition of the refined structures for the Tom1 GAT domain.	FIG
+102	105	GAT	structure_element	(A) Stereo view displaying the best-fit backbone superposition of the refined structures for the Tom1 GAT domain.	FIG
+96	100	Tom1	protein	Helices are shown in orange, whereas loops are colored in green. (B) Ribbon illustration of the Tom1 GAT domain.	FIG
+101	104	GAT	structure_element	Helices are shown in orange, whereas loops are colored in green. (B) Ribbon illustration of the Tom1 GAT domain.	FIG
+21	44	superimposed structures	experimental_method	(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).	FIG
+52	56	Tom1	protein	(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).	FIG
+57	60	GAT	structure_element	(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).	FIG
+75	79	free	protein_state	(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).	FIG
+110	116	Tollip	protein	(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).	FIG
+117	126	TBD-bound	protein_state	(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).	FIG
+161	184	superimposed structures	experimental_method	(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).	FIG
+192	196	Tom1	protein	(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).	FIG
+197	200	GAT	structure_element	(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).	FIG
+232	240	Ub-bound	protein_state	(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).	FIG
+0	3	NMR	experimental_method	NMR and refinement statistics for the Tom1 GAT domain.	TABLE
+8	29	refinement statistics	evidence	NMR and refinement statistics for the Tom1 GAT domain.	TABLE
+38	42	Tom1	protein	NMR and refinement statistics for the Tom1 GAT domain.	TABLE
+43	46	GAT	structure_element	NMR and refinement statistics for the Tom1 GAT domain.	TABLE
+0	3	NMR	experimental_method	NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS.	TABLE
+4	25	structural statistics	evidence	NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS.	TABLE
+58	62	Tom1	protein	NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS.	TABLE
+63	66	GAT	structure_element	NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS.	TABLE
+73	77	PSVS	experimental_method	NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS.	TABLE
+28	41	superimposing	experimental_method	deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures.	TABLE
+51	58	215–309	residue_range	deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures.	TABLE
+62	66	Tom1	protein	deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures.	TABLE
+67	70	GAT	structure_element	deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures.	TABLE
+102	112	structures	evidence	deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures.	TABLE