PDBe 3j9t

Electron Microscopy
6.9Å resolution

Yeast V-ATPase state 1

Released:
Source organism: Saccharomyces cerevisiae
Related structures: EMD-6284

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
Entry contents:
11 distinct polypeptide molecules
Macromolecules (11 distinct):
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
UniProt:
  • Canonical: P16140 (Residues: 1-517; Coverage: 100%)
Gene names: VAT2, VMA2, YBR1002, YBR127C
Sequence domains:
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: P31412 (Residues: 1-392; Coverage: 100%)
Gene names: VAT3, VATC, VMA5, YKL080W, YKL410
Sequence domains: V-ATPase subunit C
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
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 E 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: 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 F Chain: N
Molecule details ›
Chain: N
Length: 118 amino acids
Theoretical weight: 13.48 KDa
Source organism: Saccharomyces cerevisiae
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 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
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 c Chains: R, S, T, U, V, W, X, Y, Z, a
Molecule details ›
Chains: R, S, T, U, V, W, X, Y, Z, a
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 d Chain: Q
Molecule details ›
Chain: Q
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
Endonuclease PI-SceI Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 616 amino acids
Theoretical weight: 67.67 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P17255 (Residues: 2-1071; Coverage: 58%)
Gene names: CLS8, D1286, TFP1, VMA1, YDL185W
Sequence domains:
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
UniProt:
  • Canonical: P32563 (Residues: 1-840; Coverage: 100%)
Gene names: VPH1, YOR270C
Sequence domains: V-type ATPase 116kDa subunit family

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.9Å
Relevant EMDB volumes: EMD-6284