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-v1.2
results:
- task:
name: NER
type: token-classification
metrics:
- name: NER Precision
type: precision
value: 0.87
- name: NER Recall
type: recall
value: 0.89
- name: NER F Score
type: f_score
value: 0.88
| Feature | Description |
|---|---|
| Name | BiomedNLP-PubMedBERT-ProteinStructure-NER-v1.2 |
| 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 (19 labels for 1 components)
| Component | Labels |
|---|---|
ner |
"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 |
|---|---|---|---|---|
| "chemical" | 0.84 | 0.90 | 0.87 | 194 |
| "complex_assembly" | 0.85 | 0.76 | 0.80 | 51 |
| "evidence" | 0.74 | 0.76 | 0.75 | 106 |
| "experimental_method" | 0.77 | 0.75 | 0.76 | 116 |
| "gene" | 0.86 | 0.92 | 0.89 | 74 |
| "mutant" | 0.83 | 0.92 | 0.88 | 258 |
| "oligomeric_state" | 0.94 | 1.00 | 0.97 | 15 |
| "protein" | 0.91 | 0.93 | 0.92 | 463 |
| "protein_state" | 0.80 | 0.83 | 0.81 | 191 |
| "protein_type" | 0.85 | 0.84 | 0.84 | 166 |
| "ptm" | 0.88 | 0.76 | 0.81 | 29 |
| "residue_name" | 0.86 | 0.95 | 0.91 | 22 |
| "residue_name_number" | 0.99 | 0.99 | 0.99 | 341 |
| "residue_number" | 1.00 | 1.00 | 1.00 | 13 |
| "residue_range" | 1.00 | 0.80 | 0.89 | 10 |
| "site" | 0.83 | 0.82 | 0.82 | 99 |
| "species" | 0.96 | 0.98 | 0.97 | 44 |
| "structure_element" | 0.88 | 0.86 | 0.87 | 319 |
| "taxonomy_domain" | 0.95 | 0.97 | 0.96 | 79 |
Data and annotations
The dataset can be found here: https://huggingface.co/datasets/PDBEurope/protein_structure_NER_model_v1.2