› 6vqb

Electron Microscopy
3.6Å resolution

Mammalian V-ATPase from rat brain soluble V1 region rotational state 2 with SidK and ADP (from focused refinement)

Released:
DOI: 10.2210/pdb6vqb/pdb
PDB entry 6vqb coloured by chain, front view.
PDB entry 6vqb coloured by chain, side view.
PDB entry 6vqb coloured by chain, top view.
Source organisms:
Primary publication:
Structure of V-ATPase from the mammalian brain.
Abbas YM, Wu D, Bueler SA, Robinson CV, Rubinstein JL
Science 367 1240-1246 (2020)
PMID: 32165585
Related structures: EMD-21347

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 hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-112611 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
H(+)-transporting two-sector ATPase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 617 amino acids
Theoretical weight: 68.34 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: D4A133 (Residues: 31-647; Coverage: 95%)
Gene name: Atp6v1a
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: 56.61 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: P62815 (Residues: 1-511; Coverage: 100%)
Gene names: Atp6b2, Atp6v1b2, Vat2
Sequence domains:
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 E 1 Chains: I, J, K
Molecule details ›
Chains: I, J, K
Length: 226 amino acids
Theoretical weight: 26.17 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q6PCU2 (Residues: 1-226; Coverage: 100%)
Gene name: Atp6v1e1
Sequence domains: ATP synthase (E/31 kDa) subunit
V-type proton ATPase subunit G Chains: M, N, O
Molecule details ›
Chains: M, N, O
Length: 118 amino acids
Theoretical weight: 13.69 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q8R2H0 (Residues: 1-118; Coverage: 100%)
Gene names: Aif1, Atp6v1g2, Bat1a, Cdk2ap1-ps2, Cdk2ap1-ps3, Cdk2ap1-ps4, Cdk2ap1-ps5, Cdk2ap1-ps6, E230034O05Rik, LOC224733l-3, LOC224733l-4, LOC224733l-5, LOC224733l-6, LOC224733l-7, LOC224733l-8, Lst1, RT1-CE12, RT1-CE3, RT1-CE5, RT1-CE6, RT1-CE8, RT1-CE9, Sacm2l-ps3, Sacm2l-ps4, Sacm2l-ps5, Sacm2l-ps6, Sacm2l-ps7, Tnf
Sequence domains: Vacuolar (H+)-ATPase G subunit
Type IV secretion protein Dot Chains: Q, R, S
Molecule details ›
Chains: Q, R, S
Length: 301 amino acids
Theoretical weight: 34.69 KDa
Source organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5ZWW6 (Residues: 1-278; Coverage: 49%)
Gene name: lpg0968

Ligands and Environments

1 bound ligand:
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-21347
Expression system: Escherichia coli

Quick links

Citations

25 review citations

The assembly, regulation and function of the mitochondrial respiratory chain.
Vercellino et al. (2022)
24 more

1 mention without citation

Structure of V-ATPase from the mammalian brain.
Abbas et al. (2020)