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README.md
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---
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license: mit
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---
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license: mit
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language:
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- en
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tags:
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- biology
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- protein structure
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- token classification
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widget:
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- text: "N-terminal acetylation (Nt-acetylation), carried out by N-terminal acetyltransferases (NATs), is a conserved and primary modification of nascent peptide chains. Naa60 (also named NatF) is a recently identified NAT found only in multicellular eukaryotes. This protein was shown to locate on the Golgi apparatus and mainly catalyze the Nt-acetylation of transmembrane proteins, and it also harbors lysine Nε-acetyltransferase (KAT) activity to catalyze the acetylation of lysine ε-amine. Here, we report the crystal structures of human Naa60 (hNaa60) in complex with Acetyl-Coenzyme A (Ac-CoA) or Coenzyme A (CoA). The hNaa60 protein contains an amphipathic helix following its GNAT domain that may contribute to Golgi localization of hNaa60, and the β7-β8 hairpin adopted different conformations in the hNaa60(1-242) and hNaa60(1-199) crystal structures. Remarkably, we found that the side-chain of Phe 34 can influence the position of the coenzyme, indicating a new regulatory mechanism involving enzyme, co-factor and substrates interactions. Moreover, structural comparison and biochemical studies indicated that Tyr 97 and His 138 are key residues for catalytic reaction and that a non-conserved β3-β4 long loop participates in the regulation of hNaa60 activity."
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model-index:
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- name: BiomedNLP-PubMedBERT-ProteinStructure-NER-v2.1_onnx
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results:
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- task:
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name: NER
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type: token-classification
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metrics:
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- name: NER Precision
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type: precision
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value: 0.90
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- name: NER Recall
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type: recall
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value: 0.93
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- name: NER F Score
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type: f_score
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value: 0.91
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---
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| Feature | Description |
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| --- | --- |
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| **Name** | `BiomedNLP-PubMedBERT-ProteinStructure-NER-2.1_onnx` |
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| **Default Pipeline** | `transformer`, `ner` |
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| **Components** | `transformer`, `ner` |
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| **Vectors** | 0 keys, 0 unique vectors (0 dimensions) |
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| **Sources** | n/a |
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| **License** | n/a |
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| **Author** | [Melanie Vollmar]() |
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### Label Scheme
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<details>
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<summary>View label scheme (20 labels for 1 components)</summary>
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| Component | Labels |
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| --- | --- |
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| **`ner`** | "bond_interaction", "chemical", "complex_assembly", "evidence", "experimental_method", "gene", "mutant", "oligomeric_state", "protein", "protein_state", "protein_type", "ptm", "residue_name", "residue_name_number", "residue_number", "residue_range", "site", "species", "structure_element", "taxonomy_domain" |
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</details>
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### Scores for entity types
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| entity type | precision | recall | F1 | sample number|
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| --- | --- | --- | --- | --- |
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| "bond_interaction" | 0.94 | 0.92 | 0.93 | 41 |
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| "chemical" | 0.86 | 0.92 | 0.89 | 589 |
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| "complex_assembly" | 0.85 | 0.89 | 0.87 | 185 |
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| "evidence" | 0.83 | 0.89 | 0.86 | 392 |
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| "experimental_method" | 0.86 | 0.85 | 0.86 | 310 |
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| "gene" | 0.73 | 0.86 | 0.79 | 26 |
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| "mutant" | 0.88 | 0.94 | 0.91 | 216 |
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| "oligomeric_state" | 0.92 | 0.96 | 0.94 | 116 |
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| "protein" | 0.91 | 0.95 | 0.93 | 755 |
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| "protein_state" | 0.78 | 0.88 | 0.82 | 577 |
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| "protein_type" | 0.87 | 0.85 | 0.86 | 265 |
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| "ptm" | 0.67 | 0.69 | 0.68 | 33 |
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| "residue_name" | 0.88 | 0.95| 0.91 | 76 |
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| "residue_name_number" | 0.94 | 0.96 | 0.95 | 262 |
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| "residue_number" | 0.62 | 0.88 | 0.73 | 45 |
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| "residue_range" | 0.87 | 0.79 | 0.83 | 31 |
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| "site" | 0.88 | 0.90 | 0.89 | 245 |
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| "species" | 0.95 | 0.97 | 0.96 | 76 |
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| "structure_element" | 0.90 | 0.93 | 0.92 | 751 |
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| "taxonomy_domain" | 0.99 | 0.99 | 0.99 | 83 |
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