› 6xby

Electron Microscopy
3.79Å resolution

Cryo-EM structure of V-ATPase from bovine brain, state 2

Released:
DOI: 10.2210/pdb6xby/pdb
PDB entry 6xby coloured by chain, front view.
PDB entry 6xby coloured by chain, side view.
PDB entry 6xby coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Cryo-EM structures of intact V-ATPase from bovine brain.
Wang R, Long T, Hassan A, Wang J, Sun Y, Xie XS, Li X
Nat Commun 11 3921 (2020)
PMID: 32764564
Related structures: EMD-22122

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 30-mer (preferred)
PDBe Complex ID:
PDB-CPX-129224 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
V-type proton ATPase catalytic subunit A Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 617 amino acids
Theoretical weight: 68.42 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P31404 (Residues: 1-617; Coverage: 100%)
Gene names: ATP6A1, ATP6V1A, ATP6V1A1
Sequence domains:
V-type proton ATPase subunit B, brain isoform Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 511 amino acids
Theoretical weight: 56.64 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P31408 (Residues: 1-511; Coverage: 100%)
Gene names: ATP6B2, ATP6V1B2
Sequence domains:
V-type proton ATPase subunit C 1 Chain: G
Molecule details ›
Chain: G
Length: 382 amino acids
Theoretical weight: 44.04 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P21282 (Residues: 1-382; Coverage: 100%)
Gene names: ATP6C, ATP6V1C1, VATC
Sequence domains: V-ATPase subunit C
V-type proton ATPase subunit D Chain: H
Molecule details ›
Chain: H
Length: 247 amino acids
Theoretical weight: 28.3 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P39942 (Residues: 1-247; Coverage: 100%)
Gene names: ATP6M, ATP6V1D, VATD
Sequence domains: ATP synthase subunit D
V-type proton ATPase subunit E 1 Chains: I, J, K
Molecule details ›
Chains: I, J, K
Length: 226 amino acids
Theoretical weight: 26.18 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P11019 (Residues: 1-226; Coverage: 100%)
Gene names: ATP6E, ATP6V1E1
Sequence domains: ATP synthase (E/31 kDa) subunit
V-type proton ATPase subunit F Chain: L
Molecule details ›
Chain: L
Length: 119 amino acids
Theoretical weight: 13.42 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q28029 (Residues: 1-119; Coverage: 100%)
Gene names: ATP6S14, ATP6V1F, VATF
Sequence domains: ATP synthase (F/14-kDa) subunit
V-type proton ATPase subunit G 2 Chains: M, N, O
Molecule details ›
Chains: M, N, O
Length: 118 amino acids
Theoretical weight: 13.59 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q0VCV6 (Residues: 1-118; Coverage: 100%)
Gene name: ATP6V1G2
Sequence domains: Vacuolar (H+)-ATPase G subunit
V-type proton ATPase subunit H Chain: P
Molecule details ›
Chain: P
Length: 465 amino acids
Theoretical weight: 54.16 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: O46563 (Residues: 1-483; Coverage: 96%)
Gene name: ATP6V1H
Sequence domains:
V-type proton ATPase 116 kDa subunit a 1 Chain: a
Molecule details ›
Chain: a
Length: 838 amino acids
Theoretical weight: 96.43 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q29466 (Residues: 1-838; Coverage: 100%)
Gene names: ATP6N1, ATP6V0A1, VPP1
Sequence domains: V-type ATPase 116kDa subunit family
V-type proton ATPase 21 kDa proteolipid subunit c'' Chain: b
Molecule details ›
Chain: b
Length: 205 amino acids
Theoretical weight: 21.53 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q2TA24 (Residues: 1-205; Coverage: 100%)
Gene name: ATP6V0B
Sequence domains: ATP synthase subunit C
V-type proton ATPase subunit d 1 Chain: d
Molecule details ›
Chain: d
Length: 351 amino acids
Theoretical weight: 40.37 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P61420 (Residues: 1-351; Coverage: 100%)
Gene names: ATP6D, ATP6V0D1, VPATPD
Sequence domains: ATP synthase (C/AC39) subunit
V-type proton ATPase 16 kDa proteolipid subunit c Chains: c, g, k, l, m, n, o, p, q
Molecule details ›
Chains: c, g, k, l, m, n, o, p, q
Length: 155 amino acids
Theoretical weight: 15.73 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P23956 (Residues: 1-155; Coverage: 100%)
Gene names: ATP6C, ATP6L, ATP6V0C
Sequence domains: ATP synthase subunit C
V-type proton ATPase subunit S1 Chain: s
Molecule details ›
Chain: s
Length: 468 amino acids
Theoretical weight: 51.82 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P40682 (Residues: 1-468; Coverage: 100%)
Gene names: ATP6AP1, ATP6IP1, ATP6S1
Sequence domains:
Renin receptor Chain: r
Molecule details ›
Chain: r
Length: 351 amino acids
Theoretical weight: 39.53 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P81134 (Residues: 1-351; Coverage: 100%)
Gene names: ATP6AP2, ATP6IP2
Sequence domains: Renin receptor-like protein

Ligands and Environments

4 bound ligands:
Ligand MG 1 x MG
Ligand ADP 1 x ADP
Ligand POV 7 x POV
Ligand NAG 6 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.79Å
Relevant EMDB volumes: EMD-22122

Quick links

Citations

9 review citations

The H+-ATPase (V-ATPase): from proton pump to signaling complex in health and disease.
Eaton et al. (2021)
8 more

1 mention without citation

Multiomics Identification of Potential Targets for Alzheimer Disease and Antrocin as a Therapeutic Candidate.
Wu et al. (2021)