› 8acy

X-ray diffraction
3.5Å resolution

X-ray structure of Na+-NQR from Vibrio cholerae at 3.5 A resolution

Released:
DOI: 10.2210/pdb8acy/pdb
Model geometry
Fit model/data
PDB entry 8acy coloured by chain, front view.
PDB entry 8acy coloured by chain, side view.
PDB entry 8acy coloured by chain, top view.
Source organism: Vibrio cholerae
Primary publication:
Conformational coupling of redox-driven Na+-translocation in Vibrio cholerae NADH:quinone oxidoreductase.
Hau JL, Kaltwasser S, Muras V, Casutt MS, Vohl G, Claußen B, Steffen W, Leitner A, Bill E, Cutsail GE, DeBeer S, Vonck J, Steuber J, Fritz G
OpenAccess logo Nat Struct Mol Biol (2023)
PMID: 37710014

Function and Biology Details

Reaction catalysed: 
NADH + ubiquinone + n Na(+)(Side 1) = NAD(+) + ubiquinol + n Na(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107567 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Na(+)-translocating NADH-quinone reductase subunit A Chain: A
Molecule details ›
Chain: A
Length: 468 amino acids
Theoretical weight: 51.13 KDa
Source organism: Vibrio cholerae
Expression system: Vibrio cholerae
UniProt:
  • Canonical: A5F5X1 (Residues: 1-446; Coverage: 100%)
Gene names: VC0395_A1884, VC395_2411, nqrA
Sequence domains:
Na(+)-translocating NADH-quinone reductase subunit B Chain: B
Molecule details ›
Chain: B
Length: 415 amino acids
Theoretical weight: 45.39 KDa
Source organism: Vibrio cholerae
Expression system: Vibrio cholerae
UniProt:
  • Canonical: A5F5X0 (Residues: 1-415; Coverage: 100%)
Gene names: VC0395_A1883, VC395_2410, nqrB
Sequence domains: NQR2, RnfD, RnfE family
Na(+)-translocating NADH-quinone reductase subunit C Chain: C
Na(+)-translocating NADH-quinone reductase subunit D Chain: D
Na(+)-translocating NADH-quinone reductase subunit E Chain: E
Na(+)-translocating NADH-quinone reductase subunit F Chain: F

Ligands and Environments

6 bound ligands:
Ligand FMN 2 x FMN
Ligand RBF 1 x RBF
Ligand LMT 3 x LMT
Ligand NA 1 x NA
Ligand FES 2 x FES
Ligand FAD 1 x FAD
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 95.27Å b: 143.32Å c: 104.37Å
α: 90° β: 110.98° γ: 90°
R-values:
R R work R free
0.268 0.266 0.29
Expression system: Vibrio cholerae

Quick links

Citations

3 citation in other articles

Architecture of the RNF1 complex that drives biological nitrogen fixation.
Zhang et al. (2024)
2 more

1 mention without citation

Functionality of the Na+-translocating NADH:quinone oxidoreductase and quinol:fumarate reductase from Prevotella bryantii inferred from homology modeling.
Hau et al. (2023)