› 5vox

Electron Microscopy
6.8Å resolution

Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1)

Released:
DOI: 10.2210/pdb5vox/pdb
PDB entry 5vox coloured by chain, front view.
PDB entry 5vox coloured by chain, side view.
PDB entry 5vox coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein.
Zhao J, Beyrakhova K, Liu Y, Alvarez CP, Bueler SA, Xu L, Xu C, Boniecki MT, Kanelis V, Luo ZQ, Cygler M, Rubinstein JL
PLoS Pathog 13 e1006394 (2017)
PMID: 28570695
Related structures: EMD-8724

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 33-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147632 (preferred)
Entry contents:
16 distinct polypeptide molecules
Macromolecules (16 distinct):
Endonuclease PI-SceI Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 617 amino acids
Theoretical weight: 67.8 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P17255 (Residues: 1-1071; Coverage: 58%)
Gene names: CLS8, D1286, TFP1, VMA1, YDL185W
Sequence domains:
V-type proton ATPase subunit B Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 517 amino acids
Theoretical weight: 57.82 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P16140 (Residues: 1-517; Coverage: 100%)
Gene names: VAT2, VMA2, YBR1002, YBR127C
Sequence domains:
V-type proton ATPase subunit E Chains: G, I, K
Molecule details ›
Chains: G, I, K
Length: 233 amino acids
Theoretical weight: 26.51 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22203 (Residues: 1-233; Coverage: 100%)
Gene names: O6241, VAT5, VMA4, YOR332W
Sequence domains: ATP synthase (E/31 kDa) subunit
V-type proton ATPase subunit G Chains: H, J, L
Molecule details ›
Chains: H, J, L
Length: 114 amino acids
Theoretical weight: 12.74 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P48836 (Residues: 1-114; Coverage: 100%)
Gene names: VMA10, YHR039BC, YHR039C-A, YHR039C-B
Sequence domains: Vacuolar (H+)-ATPase G subunit
V-type proton ATPase subunit D Chain: M
Molecule details ›
Chain: M
Length: 256 amino acids
Theoretical weight: 29.24 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32610 (Residues: 1-256; Coverage: 100%)
Gene names: SYGP-ORF11, VMA8, YEL051W
Sequence domains: ATP synthase subunit D
V-type proton ATPase subunit F Chain: N
Molecule details ›
Chain: N
Length: 118 amino acids
Theoretical weight: 13.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P39111 (Residues: 1-118; Coverage: 100%)
Gene names: VMA7, YGR020C
Sequence domains: ATP synthase (F/14-kDa) subunit
V-type proton ATPase subunit C Chain: O
Molecule details ›
Chain: O
Length: 392 amino acids
Theoretical weight: 44.24 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P31412 (Residues: 1-392; Coverage: 100%)
Gene names: VAT3, VATC, VMA5, YKL080W, YKL410
Sequence domains: V-ATPase subunit C
V-type proton ATPase subunit H Chain: P
Molecule details ›
Chain: P
Length: 478 amino acids
Theoretical weight: 54.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P41807 (Residues: 1-478; Coverage: 100%)
Gene names: CLS11, VMA13, YP3085.02, YPR036W
Sequence domains:
V-type proton ATPase subunit d Chain: Q
Molecule details ›
Chain: Q
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 c'' Chain: R
Molecule details ›
Chain: R
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: S
Molecule details ›
Chain: S
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: T, U, V, W, X, Y, Z, a
Molecule details ›
Chains: T, U, V, W, X, Y, Z, a
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
V-type proton ATPase subunit a, vacuolar isoform Chain: b
Molecule details ›
Chain: b
Length: 840 amino acids
Theoretical weight: 95.63 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
V-type proton ATPase subunit e Chain: c
Molecule details ›
Chain: c
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: d
Molecule details ›
Chain: d
Length: 54 amino acids
Theoretical weight: 4.61 KDa
Source organism: Saccharomyces cerevisiae S288C
effector protein SidK Chains: e, f, g
Molecule details ›
Chains: e, f, g
Length: 573 amino acids
Theoretical weight: 65.49 KDa
Source organism: Legionella pneumophila subsp. pneumophila ATCC 43290
Expression system: Escherichia coli

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.8Å
Relevant EMDB volumes: EMD-8724
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Regulation of V-ATPase Activity and Organelle pH by Phosphatidylinositol Phosphate Lipids.
Banerjee et al. (2020)
8 more

10 mentions without citation

Drug Sequestration in Lysosomes as One of the Mechanisms of Chemoresistance of Cancer Cells and the Possibilities of Its Inhibition.
Hraběta et al. (2020)
9 more