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---
license: mit
language:
- en
tags:
- biology
- protein structure
- token classification
widget:
- 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."
model-index:
- name: BiomedNLP-PubMedBERT-ProteinStructure-NER-v2.1
results:
- task:
name: NER
type: token-classification
metrics:
- name: NER Precision
type: precision
value: 0.90
- name: NER Recall
type: recall
value: 0.92
- name: NER F Score
type: f_score
value: 0.91
---
| Feature | Description |
| --- | --- |
| **Name** | `BiomedNLP-PubMedBERT-ProteinStructure-NER-2.1` |
| **Default Pipeline** | `transformer`, `ner` |
| **Components** | `transformer`, `ner` |
| **Vectors** | 0 keys, 0 unique vectors (0 dimensions) |
| **Sources** | n/a |
| **License** | n/a |
| **Author** | [Melanie Vollmar]() |
### Label Scheme
<details>
<summary>View label scheme (20 labels for 1 components)</summary>
| Component | Labels |
| --- | --- |
| **`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" |
</details>
### Scores for entity types
| entity type | precision | recall | F1 | sample number|
| --- | --- | --- | --- | --- |
| "bond_interaction" | 0.93 | 0.88 | 0.90 | 43 |
| "chemical" | 0.89 | 0.91 | 0.90 | 761 |
| "complex_assembly" | 0.91 | 0.93 | 0.92 | 288 |
| "evidence" | 0.84 | 0.88 | 0.86 | 390 |
| "experimental_method" | 0.85 | 0.85 | 0.85 | 357 |
| "gene" | 0.79 | 0.86 | 0.82 | 43 |
| "mutant" | 0.91 | 0.97 | 0.94 | 463 |
| "oligomeric_state" | 0.93 | 0.99 | 0.96 | 142 |
| "protein" | 0.94 | 0.97 | 0.95 | 1411 |
| "protein_state" | 0.83 | 0.88 | 0.85 | 546 |
| "protein_type" | 0.85 | 0.85 | 0.85 | 414 |
| "ptm" | 0.70 | 0.70 | 0.70 | 50 |
| "residue_name" | 0.92 | 0.97| 0.94| 90 |
| "residue_name_number" | 0.95 | 0.96| 0.96 | 561 |
| "residue_number" | 0.80 | 0.97 | 0.88 | 33 |
| "residue_range" | 0.81 | 0.70 | 0.75 | 43 |
| "site" | 0.85 | 0.87 | 0.86 | 270 |
| "species" | 0.94 | 0.96 | 0.95 | 84 |
| "structure_element" | 0.91 | 0.92 | 0.92 | 992 |
| "taxonomy_domain" | 0.99 | 0.98 | 0.98 | 88 |
### Data and annotations
The dataset can be found here: https://huggingface.co/datasets/PDBEurope/protein_structure_NER_model_v2.1
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