› 6pe5

Electron Microscopy
3.2Å resolution

Yeast Vo motor in complex with 2 VopQ molecules

Released:
DOI: 10.2210/pdb6pe5/pdb
PDB entry 6pe5 coloured by chain, front view.
PDB entry 6pe5 coloured by chain, side view.
PDB entry 6pe5 coloured by chain, top view.
Source organisms:
Primary publication:
A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM.
Peng W, Casey AK, Fernandez J, Carpinone EM, Servage KA, Chen Z, Li Y, Tomchick DR, Starai VJ, Orth K
Nat Struct Mol Biol 27 589-597 (2020)
PMID: 32424347
Related structures: EMD-20323

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero heptadecamer (preferred)
PDBe Complex ID:
PDB-CPX-143032 (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (9 distinct):
V-type proton ATPase subunit a, vacuolar isoform Chain: A
Molecule details ›
Chain: A
Length: 1012 amino acids
Theoretical weight: 115.13 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32563 (Residues: 1-840; Coverage: 100%)
Gene names: VPH1, YOR270C
Sequence domains: V-type ATPase 116kDa subunit family
V0 assembly protein 1 Chain: B
Molecule details ›
Chain: B
Length: 265 amino acids
Theoretical weight: 29.69 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53262 (Residues: 1-265; Coverage: 100%)
Gene names: VOA1, YGR106C
Sequence domains: V0 complex accessory subunit Ac45/VOA1 transmembrane domain
V-type proton ATPase subunit d Chain: D
Molecule details ›
Chain: D
Length: 345 amino acids
Theoretical weight: 39.82 KDa
Source organism: Saccharomyces cerevisiae S288C
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 e Chain: E
Molecule details ›
Chain: E
Length: 73 amino acids
Theoretical weight: 8.39 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q3E7B6 (Residues: 1-73; Coverage: 100%)
Gene names: CWH36, LDB10, VMA9, YCL005W-A
Sequence domains: ATP synthase subunit H
V-type proton ATPase subunit f Chain: F
Molecule details ›
Chain: F
Length: 85 amino acids
Theoretical weight: 9.37 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C5R9 (Residues: 1-85; Coverage: 100%)
Gene name: YPR170W-B
V-type proton ATPase subunit c'' Chain: G
Molecule details ›
Chain: G
Length: 213 amino acids
Theoretical weight: 22.61 KDa
Source organism: Saccharomyces cerevisiae S288C
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: H
Molecule details ›
Chain: H
Length: 164 amino acids
Theoretical weight: 17.05 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32842 (Residues: 1-164; Coverage: 100%)
Gene names: CLS9, P1064, TFP3, VMA11, YPL234C
Sequence domains: ATP synthase subunit C
V-type proton ATPase subunit c Chains: I, J, K, L, M, N, O, P
Molecule details ›
Chains: I, J, K, L, M, N, O, P
Length: 160 amino acids
Theoretical weight: 16.36 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25515 (Residues: 1-160; Coverage: 100%)
Gene names: CLS7, CUP5, GEF2, VMA3, YEL027W
Sequence domains: ATP synthase subunit C
Cation transporter Chains: Q, R
Molecule details ›
Chains: Q, R
Length: 513 amino acids
Theoretical weight: 55.42 KDa
Source organism: Vibrio parahaemolyticus
Expression system: Escherichia coli

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-20323
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Targeting lysosomes in human disease: from basic research to clinical applications.
Cao et al. (2021)
2 more