V-type proton ATPase subunit B (VMA2) is a 517-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P16140.
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The mean pLDDT of this model is 85.8 (confident 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 | 58% |
| 70 to 90 | Confident: backbone generally right | 32% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 7% |
What pLDDT means and how to read it
Non-catalytic subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (PubMed:2141385). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments (PubMed:2141385)
V-ATPase is a heteromultimeric enzyme composed of a peripheral catalytic V1 complex (components A to H) attached to an integral membrane V0 proton pore complex (components: a, c, c', c'', d, e, f and VOA1) (PubMed:18055462, PubMed:25971514, PubMed:27295975). Interacts with RAV1 and RAV2 components of the RAVE complex, which are essential for the stability and assembly of V-ATPase (PubMed:11283612)
Vacuole membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9COP | EM | 2.7 Å | B/F=1-517 |
| 7TMO | EM | 3.3 Å | B/D/F=1-517 |
| 7TMP | EM | 3.3 Å | B/D/F=1-517 |
| 7TMQ | EM | 3.3 Å | B/D/F=1-517 |
| 7TMM | EM | 3.5 Å | B/D/F=1-517 |
| 7TMR | EM | 3.5 Å | B/D/F=1-517 |
| 7FDE | EM | 3.8 Å | B/D/F=1-517 |
| 7FDA | EM | 4.2 Å | B/D/F=1-517 |
| 7FDB | EM | 4.8 Å | B/D/F=1-517 |
| 5D80 | X-ray | 6.2 Å | D/E/F/d/e/f=1-517 |
| 6O7V | EM | 6.6 Å | B/D/F=1-517 |
| 7FDC | EM | 6.6 Å | B/D/F=1-517 |
| 5VOX | EM | 6.8 Å | B/D/F=1-517 |
| 3J9T | EM | 6.9 Å | B/D/F=1-517 |
| 5BW9 | X-ray | 7.0 Å | D/E/F/d/e/f=1-517 |
| 6O7W | EM | 7.0 Å | B/D/F=1-517 |
| 3J9U | EM | 7.6 Å | B/D/F=1-517 |
| 5VOZ | EM | 7.6 Å | B/D/F=1-517 |
| 5VOY | EM | 7.9 Å | B/D/F=1-517 |
| 3J9V | EM | 8.3 Å | B/D/F=1-517 |
Showing 20 of 21 experimental structures (best resolution first).
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