metadata
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-v3.1
results:
- task:
name: NER
type: token-classification
metrics:
- name: NER Precision
type: precision
value: 0.91
- 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-3.1 |
| 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
View label scheme (20 labels for 1 components)
| 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" |
Scores for entity types
| entity type | precision | recall | F1 | sample number |
|---|---|---|---|---|
| "bond_interaction" | 0.82 | 0.91 | 0.86 | 66 |
| "chemical" | 0.92 | 0.91 | 0.92 | 1046 |
| "complex_assembly" | 0.89 | 0.90 | 0.90 | 320 |
| "evidence" | 0.89 | 0.88 | 0.89 | 513 |
| "experimental_method" | 0.80 | 0.82 | 0.81 | 451 |
| "gene" | 0.79 | 0.65 | 0.71 | 63 |
| "mutant" | 0.92 | 0.94 | 0.93 | 548 |
| "oligomeric_state" | 0.96 | 1.00 | 0.98 | 149 |
| "protein" | 0.96 | 0.96 | 0.96 | 1769 |
| "protein_state" | 0.86 | 0.88 | 0.87 | 727 |
| "protein_type" | 0.85 | 0.88 | 0.87 | 585 |
| "ptm" | 0.85 | 0.79 | 0.82 | 77 |
| "residue_name" | 0.74 | 0.96 | 0.84 | 108 |
| "residue_name_number" | 0.96 | 0.98 | 0.97 | 689 |
| "residue_number" | 0.70 | 0.73 | 0.71 | 22 |
| "residue_range" | 0.89 | 0.86 | 0.87 | 93 |
| "site" | 0.88 | 0.90 | 0.89 | 336 |
| "species" | 0.95 | 0.95 | 0.95 | 152 |
| "structure_element" | 0.91 | 0.92 | 0.91 | 1278 |
| "taxonomy_domain" | 0.98 | 0.98 | 0.98 | 117 |
Data and annotations
The dataset can be found here: https://huggingface.co/datasets/PDBEurope/protein_structure_NER_model_v3.1