› 3a5d

X-ray diffraction
4.8Å resolution

Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase

Released:
DOI: 10.2210/pdb3a5d/pdb
PDB entry 3a5d coloured by chain, front view.
PDB entry 3a5d coloured by chain, side view.
PDB entry 3a5d coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase.
Numoto N, Hasegawa Y, Takeda K, Miki K
EMBO Rep 10 1228-34 (2009)
PMID: 19779483

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 octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131513 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
V-type ATP synthase alpha chain Chains: A, B, C, I, J, K
Molecule details ›
Chains: A, B, C, I, J, K
Length: 578 amino acids
Theoretical weight: 63.7 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56403 (Residues: 1-578; Coverage: 100%)
Gene names: TTHA1273, atpA
Sequence domains:
V-type ATP synthase beta chain Chains: D, E, F, L, M, N
Molecule details ›
Chains: D, E, F, L, M, N
Length: 478 amino acids
Theoretical weight: 53.22 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56404 (Residues: 1-478; Coverage: 100%)
Gene names: TTHA1272, atpB
Sequence domains:
V-type ATP synthase subunit D Chains: G, O
Molecule details ›
Chains: G, O
Length: 223 amino acids
Theoretical weight: 24.72 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: O87880 (Residues: 1-223; Coverage: 100%)
Gene names: TTHA1271, atpD, vatD
Sequence domains: ATP synthase subunit D
V-type ATP synthase subunit F Chains: H, P
Molecule details ›
Chains: H, P
Length: 104 amino acids
Theoretical weight: 11.29 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P74903 (Residues: 1-104; Coverage: 100%)
Gene names: TTHA1274, atpF, vatF
Sequence domains: ATP synthase (F/14-kDa) subunit

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P321
Unit cell:
a: 380.701Å b: 380.701Å c: 147.971Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.441 0.441 0.454

Quick links

Citations

8 review citations

Eukaryotic V-ATPase: novel structural findings and functional insights.
Marshansky et al. (2014)
7 more

6 mentions without citation

Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase.
Numoto et al. (2009)
5 more