› 6vq6

Electron Microscopy
3.9Å resolution

Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models)

Released:
DOI: 10.2210/pdb6vq6/pdb
PDB entry 6vq6 coloured by chain, front view.
PDB entry 6vq6 coloured by chain, side view.
PDB entry 6vq6 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-21317

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 34-mer (preferred)
PDBe Complex ID:
PDB-CPX-109161 (preferred)
Entry contents:
16 distinct polypeptide molecules
Macromolecules (16 distinct):
V-type proton ATPase catalytic subunit A Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 617 amino acids
Theoretical weight: 68.34 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 C 1 Chain: G
Molecule details ›
Chain: G
Length: 382 amino acids
Theoretical weight: 43.96 KDa
Source organism: Rattus norvegicus
UniProt:
  • Canonical: Q5FVI6 (Residues: 1-382; Coverage: 100%)
Gene name: Atp6v1c1
Sequence domains: V-ATPase subunit C
V-type proton ATPase subunit D Chain: H
Molecule details ›
Chain: H
Length: 247 amino acids
Theoretical weight: 28.36 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 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 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
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

2 bound ligands:
Ligand ADP 1 x ADP
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-21317
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

5 mentions without citation

In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.
Chavez et al. (2022)
4 more