V-type proton ATPase subunit a, vacuolar isoform (VPH1) is a 840-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P32563.
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The mean pLDDT of this model is 81.0 (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 | 27% |
| 70 to 90 | Confident: backbone generally right | 57% |
| 50 to 70 | Low: treat with caution | 6% |
| Below 50 | Very low: often disordered regions | 10% |
What pLDDT means and how to read it
Subunit of the V0 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:11278748, PubMed:1491220, PubMed:8798414). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments (PubMed:11278748, PubMed:1491220). Is present only in vacuolar V-ATPase complexes; enzymes containing this subunit have a 4-fold higher ratio of proton transport to ATP hydrolysis than complexes containing the Golgi/endosomal isoform and undergo reversible dissociation of V1 and V0 in response to glucose depletion (PubMed:11278748, PubMed:8798414)
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)
Vacuole membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8EAS | EM | 2.6 Å | a=1-840 |
| 6M0R | EM | 2.7 Å | A=3-827 |
| 7TAP | EM | 2.8 Å | A=1-840 |
| 6PE4 | EM | 3.1 Å | A=1-840 |
| 8EAU | EM | 3.1 Å | a=1-840 |
| 6O7T | EM | 3.2 Å | a=1-840 |
| 6PE5 | EM | 3.2 Å | A=1-840 |
| 7TAO | EM | 3.2 Å | A=1-840 |
| 9E7L | EM | 3.33 Å | A=1-840 |
| 9E76 | EM | 3.4 Å | A=1-840 |
| 6C6L | EM | 3.5 Å | A=1-840 |
| 7TMR | EM | 3.5 Å | a=1-840 |
| 6M0S | EM | 3.6 Å | A=3-827 |
| 9MJ4 | EM | 3.7 Å | A=1-840 |
| 7TMS | EM | 3.8 Å | a=1-840 |
| 7TMT | EM | 3.8 Å | a=1-840 |
| 5TJ5 | EM | 3.9 Å | A=400-829 |
| 7FDA | EM | 4.2 Å | Q=1-840 |
| 7FDB | EM | 4.8 Å | Q=1-840 |
| 7FDC | EM | 6.6 Å | Q=1-840 |
Showing 20 of 31 experimental structures (best resolution first).
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