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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-v3.1 |
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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: 0.91 |
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- name: NER Recall |
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type: recall |
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value: 0.92 |
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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-3.1` | |
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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" | 0.82 | 0.91 | 0.86 | 66 | |
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| "chemical" | 0.92 | 0.91 | 0.92 | 1046 | |
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| "complex_assembly" | 0.89 | 0.90 | 0.90 | 320 | |
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| "evidence" | 0.89 | 0.88 | 0.89 | 513 | |
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| "experimental_method" | 0.80 | 0.82 | 0.81 | 451 | |
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| "gene" | 0.79 | 0.65 | 0.71 | 63 | |
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| "mutant" | 0.92 | 0.94 | 0.93 | 548 | |
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| "oligomeric_state" | 0.96 | 1.00 | 0.98 | 149 | |
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| "protein" | 0.96 | 0.96 | 0.96 | 1769 | |
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| "protein_state" | 0.86 | 0.88 | 0.87 | 727 | |
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| "protein_type" | 0.85 | 0.88 | 0.87 | 585 | |
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| "ptm" | 0.85 | 0.79 | 0.82 | 77 | |
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| "residue_name" | 0.74 | 0.96 | 0.84 | 108 | |
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| "residue_name_number" | 0.96 | 0.98 | 0.97 | 689 | |
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| "residue_number" | 0.70 | 0.73 | 0.71 | 22 | |
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| "residue_range" | 0.89 | 0.86 | 0.87 | 93 | |
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| "site" | 0.88 | 0.90 | 0.89 | 336 | |
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| "species" | 0.95 | 0.95 | 0.95 | 152 | |
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| "structure_element" | 0.91 | 0.92 | 0.91 | 1278 | |
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| "taxonomy_domain" | 0.98 | 0.98 | 0.98 | 117 | |
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### Data and annotations |
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The dataset can be found here: https://huggingface.co/datasets/PDBEurope/protein_structure_NER_model_v3.1 |
