› 5d80

X-ray diffraction
6.2Å resolution

Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form

Released:
DOI: 10.2210/pdb5d80/pdb
PDB entry 5d80 coloured by chain, front view.
PDB entry 5d80 coloured by chain, side view.
PDB entry 5d80 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Crystal structure of yeast V1-ATPase in the autoinhibited state.
Oot RA, Kane PM, Berry EA, Wilkens S
EMBO J 35 1694-706 (2016)
PMID: 27295975

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 pentadecamer (preferred)
PDBe Complex ID:
PDB-CPX-147638 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (7 distinct):
Endonuclease PI-SceI Chains: A, B, C, a, b, c
Molecule details ›
Chains: A, B, C, a, b, c
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: D, E, F, d, e, f
Molecule details ›
Chains: D, E, F, d, e, 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 H Chains: H, h
Molecule details ›
Chains: H, h
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 G Chains: J, L, N, j, l, n
Molecule details ›
Chains: J, L, N, j, l, n
Length: 122 amino acids
Theoretical weight: 13.74 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P48836 (Residues: 2-114; Coverage: 99%)
Gene names: VMA10, YHR039BC, YHR039C-A, YHR039C-B
Sequence domains: Vacuolar (H+)-ATPase G subunit
V-type proton ATPase subunit E Chains: I, K, M, i, k, m
Molecule details ›
Chains: I, K, M, i, k, m
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 D Chains: G, g
Molecule details ›
Chains: G, g
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 Chains: O, o
Molecule details ›
Chains: O, o
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

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: C2
Unit cell:
a: 468.02Å b: 159.65Å c: 248.27Å
α: 90° β: 113.75° γ: 90°
R-values:
R R work R free
0.257 0.254 0.302

Quick links

Citations

8 review citations

Breaking up and making up: The secret life of the vacuolar H+ -ATPase.
Oot et al. (2017)
7 more

6 mentions without citation

Regulation and function of V-ATPases in physiology and disease.
Collins et al. (2020)
5 more