Ubiquitin carboxyl-terminal hydrolase 8 (UBP8) is a 471-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P50102.
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The mean pLDDT of this model is 91.7 (very high overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 78% |
| 70 to 90 | Confident: backbone generally right | 18% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
Histone deubiquitinating enzyme component of the transcription coactivator SAGA complex (PubMed:14563679, PubMed:14660634, PubMed:25216679, PubMed:28918903). SAGA acts as a general cofactor required for essentially all RNA polymerase II transcription (PubMed:10864329, PubMed:25216679, PubMed:28918903). At the promoters, SAGA is required for transcription pre-initiation complex (PIC) recruitment. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (via core/TAF module) and promoter selectivity, interaction with transcription activators (via Tra1/SPT module), and chromatin modification through histone acetylation (via HAT module) and…
Component of the 1.8 MDa SAGA (Spt-Ada-Gcn5 acetyltransferase) complex, which is composed of 19 subunits TRA1, SPT7, TAF5, NGG1/ADA3, SGF73, SPT20/ADA5, SPT8, TAF12, TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and SUS1 (PubMed:12052880, PubMed:14660634, PubMed:15657441, PubMed:31969703). The SAGA complex is composed of 4 modules, namely the HAT (histone acetyltransferase)…
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3MHS | X-ray | 1.89 Å | A=1-471 |
| 4FK5 | X-ray | 2.03 Å | A=1-471 |
| 6AQR | X-ray | 2.1 Å | A=1-471 |
| 4WA6 | X-ray | 2.36 Å | A/D=1-471 |
| 3MHH | X-ray | 2.45 Å | A=1-471 |
| 4FIP | X-ray | 2.69 Å | A/E=1-471 |
| 3M99 | X-ray | 2.7 Å | A=1-471 |
| 4FJC | X-ray | 2.83 Å | A/E=1-471 |
| 6T9L | EM | 3.6 Å | K=1-471 |
| 4ZUX | X-ray | 3.82 Å | U/Z/e/j=1-471 |
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