6vqc

Electron Microscopy
3.8Å resolution

Mammalian V-ATPase from rat brain membrane-embedded Vo region rotational state 1 (from focused refinement)

Released:
Source organism: Rattus norvegicus
Primary publication:
Structure of V-ATPase from the mammalian brain.
Science 367 1240-1246 (2020)
PMID: 32165585
Related structures: EMD-21348

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-109162 (preferred)
Entry contents:
10 distinct polypeptide molecules
Macromolecules (10 distinct):
V-type proton ATPase subunit D Chain: H
Molecule details ›
Chain: H
Length: 247 amino acids
Theoretical weight: 28.36 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q6P503 (Residues: 1-247; Coverage: 100%)
Gene name: Atp6v1d
Sequence domains: ATP synthase subunit D
V-type proton ATPase subunit F Chain: L
Molecule details ›
Chain: L
Length: 119 amino acids
Theoretical weight: 13.39 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P50408 (Residues: 1-119; Coverage: 100%)
Gene names: Atp6s14, Atp6v1f, Vatf
Sequence domains: ATP synthase (F/14-kDa) subunit
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: Rattus norvegicus
UniProt:
  • Canonical: P25286 (Residues: 1-838; Coverage: 100%)
Gene names: Atp6n1, Atp6v0a1, Vpp1
Sequence domains: V-type ATPase 116kDa subunit family
V-ATPase proteolipid subunit C-like domain-containing protein Chain: b
Molecule details ›
Chain: b
Length: 205 amino acids
Theoretical weight: 21.62 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: B0K022 (Residues: 1-205; Coverage: 100%)
Gene names: Atp6v0b, Atp6v0b_predicted, rCG_50448
Sequence domains: ATP synthase subunit C
V-type proton ATPase subunit S1 Chain: c
Molecule details ›
Chain: c
Length: 463 amino acids
Theoretical weight: 51.16 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: O54715 (Residues: 1-463; Coverage: 100%)
Gene names: Atp6ap1, Atp6ip1, Atp6s1
Sequence domains:
V-type proton ATPase subunit Chain: d
Molecule details ›
Chain: d
Length: 351 amino acids
Theoretical weight: 40.34 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q5M7T6 (Residues: 1-351; Coverage: 100%)
Gene names: Atp6v0d1, rCG_51062
Sequence domains: ATP synthase (C/AC39) subunit
V-type proton ATPase subunit e 2 Chain: e
Molecule details ›
Chain: e
Length: 81 amino acids
Theoretical weight: 9.2 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q5EB76 (Residues: 1-81; Coverage: 100%)
Gene name: Atp6v0e2
Sequence domains: ATP synthase subunit H
Similar to RIKEN cDNA 1110020A23 Chain: f
Molecule details ›
Chain: f
Length: 98 amino acids
Theoretical weight: 11 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: D3ZIM6 (Residues: 1-71; Coverage: 100%)
Gene names: C10h17orf49, Rnasek
V-type proton ATPase 16 kDa proteolipid subunit c Chains: g, h, i, j, k, l, m, n, o
Molecule details ›
Chains: g, h, i, j, k, l, m, n, o
Length: 155 amino acids
Theoretical weight: 15.82 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P63081 (Residues: 1-155; Coverage: 100%)
Gene names: Atp6c, Atp6l, Atp6v0c, Atpl
Sequence domains: ATP synthase subunit C
Renin receptor Chain: p
Molecule details ›
Chain: p
Length: 350 amino acids
Theoretical weight: 39.12 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q6AXS4 (Residues: 1-350; Coverage: 100%)
Gene names: Atp6ap2, Atp6ip2
Sequence domains: Renin receptor-like protein

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-21348