› 7fdc

Electron Microscopy
6.6Å resolution

CryoEM Structures of Reconstituted V-ATPase, state3

Released:
DOI: 10.2210/pdb7fdc/pdb
PDB entry 7fdc coloured by chain, front view.
PDB entry 7fdc coloured by chain, side view.
PDB entry 7fdc coloured by chain, top view.
Source organisms:
Primary publication:
CryoEM Structures of Reconstituted V-ATPase and Oxr1-bound V1 Reveal a Novel Mechanism of Regulation.
Khan MM, Lee S, Oot RA, Couoh-Cardel S, Kim H, Wilkens S, Roh SH
EMBO J. (2021)
Related structures: EMD-31540

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-143028 (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: 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 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
Expression system: Escherichia coli
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: 469 amino acids
Theoretical weight: 53.89 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: P41807 (Residues: 1-359; Coverage: 75%)
  • Canonical: Q9UI12 (Residues: 356-465; Coverage: 23%)
Gene names: ATP6V1H, CGI-11, CLS11, VMA13, YP3085.02, YPR036W
Sequence domains:
V-type proton ATPase subunit a, vacuolar isoform Chain: Q
Molecule details ›
Chain: Q
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 d Chain: S
Molecule details ›
Chain: S
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: T
Molecule details ›
Chain: T
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: U
Molecule details ›
Chain: U
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: V, W, X, Y, Z, a, b, c
Molecule details ›
Chains: V, W, X, Y, Z, a, b, c
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 e Chain: d
Molecule details ›
Chain: d
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
V0 assembly protein 1 Chain: e
Molecule details ›
Chain: e
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 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

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.6Å
Relevant EMDB volumes: EMD-31540
Expression system: Escherichia coli

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