|
--- |
|
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_onnx |
|
results: |
|
- task: |
|
name: NER |
|
type: token-classification |
|
metrics: |
|
- name: NER Precision |
|
type: precision |
|
value: 0.90 |
|
- name: NER Recall |
|
type: recall |
|
value: 0.93 |
|
- name: NER F Score |
|
type: f_score |
|
value: 0.91 |
|
--- |
|
| Feature | Description | |
|
| --- | --- | |
|
| **Name** | `BiomedNLP-PubMedBERT-ProteinStructure-NER-2.1_onnx` | |
|
| **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" | 0.94 | 0.92 | 0.93 | 41 | |
|
| "chemical" | 0.86 | 0.92 | 0.89 | 589 | |
|
| "complex_assembly" | 0.85 | 0.89 | 0.87 | 185 | |
|
| "evidence" | 0.83 | 0.89 | 0.86 | 392 | |
|
| "experimental_method" | 0.86 | 0.85 | 0.86 | 310 | |
|
| "gene" | 0.73 | 0.86 | 0.79 | 26 | |
|
| "mutant" | 0.88 | 0.94 | 0.91 | 216 | |
|
| "oligomeric_state" | 0.92 | 0.96 | 0.94 | 116 | |
|
| "protein" | 0.91 | 0.95 | 0.93 | 755 | |
|
| "protein_state" | 0.78 | 0.88 | 0.82 | 577 | |
|
| "protein_type" | 0.87 | 0.85 | 0.86 | 265 | |
|
| "ptm" | 0.67 | 0.69 | 0.68 | 33 | |
|
| "residue_name" | 0.88 | 0.95| 0.91 | 76 | |
|
| "residue_name_number" | 0.94 | 0.96 | 0.95 | 262 | |
|
| "residue_number" | 0.62 | 0.88 | 0.73 | 45 | |
|
| "residue_range" | 0.87 | 0.79 | 0.83 | 31 | |
|
| "site" | 0.88 | 0.90 | 0.89 | 245 | |
|
| "species" | 0.95 | 0.97 | 0.96 | 76 | |
|
| "structure_element" | 0.90 | 0.93 | 0.92 | 751 | |
|
| "taxonomy_domain" | 0.99 | 0.99 | 0.99 | 83 | |
|
|
