› 9e76

Electron Microscopy
3.4Å resolution

Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25

Released:
DOI: 10.2210/pdb9e76/pdb
PDB entry 9e76 coloured by chain, front view.
PDB entry 9e76 coloured by chain, side view.
PDB entry 9e76 coloured by chain, top view.
Source organisms:
Primary publication:
Monoclonal nanobodies alter the activity and assembly of the yeast vacuolar H+-ATPase.
Knight K, Park JB, Oot RA, Khan MM, Roh SH, Wilkens S
bioRxiv (2025)
PMID: 39829782
Related structures: EMD-47659

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
PDBe Complex ID:
PDB-CPX-284915 (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (9 distinct):
V-type proton ATPase subunit d Chain: B
Molecule details ›
Chain: B
Length: 345 amino acids
Theoretical weight: 39.82 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32366 (Residues: 1-345; Coverage: 100%)
Gene names: L9324.8, VMA6, YLR447C
Sequence domains: ATP synthase (C/AC39) subunit
V-type proton ATPase subunit c'' Chain: C
Molecule details ›
Chain: C
Length: 213 amino acids
Theoretical weight: 22.61 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23968 (Residues: 1-213; Coverage: 100%)
Gene names: PPA1, VMA16, YHR026W
Sequence domains: ATP synthase subunit C
V-type proton ATPase subunit c' Chain: D
V-type proton ATPase subunit c Chains: E, F, G, H, I, J, K, L
V-type proton ATPase subunit e Chain: M
V0 assembly protein 1 Chain: N
V-type proton ATPase subunit f Chain: O
Nanobody 1WVA25 Chains: Q, R, S, T
V-type proton ATPase subunit a, vacuolar isoform Chain: A

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.4Å
Relevant EMDB volumes: EMD-47659
Expression system: Escherichia coli

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