› 7tms

Electron Microscopy
3.8Å resolution

V-ATPase from Saccharomyces cerevisiae, State 2

Released:
DOI: 10.2210/pdb7tms/pdb
PDB entry 7tms coloured by chain, front view.
PDB entry 7tms coloured by chain, side view.
PDB entry 7tms coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Coordinated conformational changes in the V1 complex during V-ATPase reversible dissociation.
Vasanthakumar T, Keon KA, Bueler SA, Jaskolka MC, Rubinstein JL
Nat Struct Mol Biol 29 430-439 (2022)
PMID: 35469063
Related structures: EMD-26001

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 31-mer (preferred)
PDBe Complex ID:
PDB-CPX-105536 (preferred)
Entry contents:
16 distinct polypeptide molecules
Macromolecules (16 distinct):
V-type proton ATPase catalytic subunit A Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 617 amino acids
Theoretical weight: 67.8 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: B3LH69 (Residues: 1-617; Coverage: 100%)
Gene name: SCRG_00677
Sequence domains:
Vacuolar proton pump 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
UniProt:
  • Canonical: A0A6A5Q585 (Residues: 1-517; Coverage: 100%)
Gene names: GI527_G0000335, VMA2
Sequence domains:
VMA4 isoform 1 Chains: G, I, K
Molecule details ›
Chains: G, I, K
Length: 233 amino acids
Theoretical weight: 26.51 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: A0A6A5Q7Y8 (Residues: 1-233; Coverage: 100%)
Gene names: GI527_G0005702, VMA4
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
UniProt:
  • Canonical: P48836 (Residues: 1-114; Coverage: 100%)
Gene names: VMA10, YHR039BC, YHR039C-A, YHR039C-B
Sequence domains: Vacuolar (H+)-ATPase G subunit
VMA8 isoform 1 Chain: M
Molecule details ›
Chain: M
Length: 256 amino acids
Theoretical weight: 29.24 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: A0A6A5Q1W2 (Residues: 1-256; Coverage: 100%)
Gene names: GI527_G0001727, VMA8
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
UniProt:
  • Canonical: A0A6A5PYF6 (Residues: 1-118; Coverage: 100%)
Gene names: GI527_G0002441, VMA7
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
UniProt:
  • Canonical: A0A6A5PTP1 (Residues: 1-392; Coverage: 100%)
Gene names: GI527_G0003558, VMA5
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
UniProt:
  • Canonical: P41807 (Residues: 1-478; Coverage: 100%)
Gene names: CLS11, VMA13, YP3085.02, YPR036W
Sequence domains:
V-type proton ATPase subunit a, vacuolar isoform Chain: a
Molecule details ›
Chain: a
Length: 840 amino acids
Theoretical weight: 95.63 KDa
Source organism: Saccharomyces cerevisiae
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
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 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 d Chain: d
Molecule details ›
Chain: d
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 e Chain: e
Molecule details ›
Chain: e
Length: 73 amino acids
Theoretical weight: 8.39 KDa
Source organism: Saccharomyces cerevisiae
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
UniProt:
  • Canonical: P0C5R9 (Residues: 1-85; Coverage: 100%)
Gene name: YPR170W-B
V-type proton ATPase subunit c Chains: g, h, i, j, k, l, m, n
Molecule details ›
Chains: g, h, i, j, k, l, m, n
Length: 160 amino acids
Theoretical weight: 16.36 KDa
Source organism: Saccharomyces cerevisiae
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 c' Chain: o
Molecule details ›
Chain: o
Length: 164 amino acids
Theoretical weight: 17.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32842 (Residues: 1-164; Coverage: 100%)
Gene names: CLS9, P1064, TFP3, VMA11, YPL234C
Sequence domains: ATP synthase subunit C

Ligands and Environments

1 bound ligand:
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-26001

Quick links

Citations

1 review citation

The Plant V-ATPase.
Seidel T. (2022)
4 other articles

56 mentions without citation

Structure and function of the human calcium-sensing receptor: insights from natural and engineered mutations and allosteric modulators.
Hu et al. (2007)
55 more