› 6koe

X-ray diffraction
3.75Å resolution

X-ray Structure of the proton-pumping cytochrome aa3-600 menaquinol oxidase from Bacillus subtilis

Released:
DOI: 10.2210/pdb6koe/pdb
PDB entry 6koe coloured by chain, front view.
PDB entry 6koe coloured by chain, side view.
PDB entry 6koe coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Structure of the cytochrome aa3 -600 heme-copper menaquinol oxidase bound to inhibitor HQNO shows TM0 is part of the quinol binding site.
Xu J, Ding Z, Liu B, Yi SM, Li J, Zhang Z, Liu Y, Li J, Liu L, Zhou A, Gennis RB, Zhu J
Proc Natl Acad Sci U S A 117 872-876 (2020)
PMID: 31888984

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-543172 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Quinol oxidase subunit 1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 655 amino acids
Theoretical weight: 74.72 KDa
Source organism: Bacillus subtilis
Expression system: Bacillus subtilis
UniProt:
  • Canonical: P34956 (Residues: 1-649; Coverage: 100%)
Gene names: BSU38160, ipa-38d, qoxB
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Quinol oxidase subunit 2 Chains: B, F
Molecule details ›
Chains: B, F
Length: 296 amino acids
Theoretical weight: 33.59 KDa
Source organism: Bacillus subtilis
Expression system: Bacillus subtilis
UniProt:
  • Canonical: P34957 (Residues: 26-321; Coverage: 100%)
Gene names: BSU38170, ipa-37d, qoxA
Sequence domains:
Quinol oxidase subunit 3 Chains: C, G
Molecule details ›
Chains: C, G
Length: 204 amino acids
Theoretical weight: 22.69 KDa
Source organism: Bacillus subtilis
Expression system: Bacillus subtilis
UniProt:
  • Canonical: P34958 (Residues: 1-204; Coverage: 100%)
Gene names: BSU38150, ipa-39d, qoxC
Sequence domains: Cytochrome c oxidase subunit III
Quinol oxidase subunit 4 Chains: D, H
Molecule details ›
Chains: D, H
Length: 124 amino acids
Theoretical weight: 12.4 KDa
Source organism: Bacillus subtilis
Expression system: Bacillus subtilis
UniProt:
  • Canonical: P34959 (Residues: 48-124; Coverage: 62%)
Gene names: BSU38140, ipa-40d, qoxD
Sequence domains: Prokaryotic Cytochrome C oxidase subunit IV

Ligands and Environments

3 bound ligands:
Ligand HEA 4 x HEA
Ligand CU 2 x CU
Ligand HQO 2 x HQO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 112.988Å b: 162.11Å c: 149.509Å
α: 90° β: 109.02° γ: 90°
R-values:
R R work R free
0.347 0.347 0.368
Expression system: Bacillus subtilis

Quick links

Citations

4 review citations

Architecture of bacterial respiratory chains.
Kaila et al. (2021)
3 more

1 mention without citation

Structure of the cytochrome aa 3 -600 heme-copper menaquinol oxidase bound to inhibitor HQNO shows TM0 is part of the quinol binding site.
Xu et al. (2020)