› 3dtu

X-ray diffraction
2.15Å resolution

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides complexed with deoxycholic acid

Released:
DOI: 10.2210/pdb3dtu/pdb
PDB entry 3dtu coloured by chain, front view.
PDB entry 3dtu coloured by chain, side view.
PDB entry 3dtu coloured by chain, top view.
Source organism: Cereibacter sphaeroides
Primary publication:
A conserved steroid binding site in cytochrome C oxidase.
Qin L, Mills DA, Buhrow L, Hiser C, Ferguson-Miller S
Biochemistry 47 9931-3 (2008)
PMID: 18759498

Function and Biology Details

Reaction catalysed: 
4 ferrocytochrome c + O(2) + 8 H(+)(Side 1) = 4 ferricytochrome c + 4 H(2)O(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152619 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cytochrome c oxidase subunit 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 566 amino acids
Theoretical weight: 63.2 KDa
Source organism: Cereibacter sphaeroides
Expression system: Cereibacter sphaeroides
UniProt:
  • Canonical: P33517 (Residues: 1-566; Coverage: 100%)
Gene name: ctaD
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Structure domains: Cytochrome c oxidase-like, subunit I domain
Cytochrome c oxidase subunit 2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 262 amino acids
Theoretical weight: 29.37 KDa
Source organism: Cereibacter sphaeroides
Expression system: Cereibacter sphaeroides
UniProt:
  • Canonical: Q03736 (Residues: 26-281; Coverage: 92%)
Gene names: coxII, ctaB, ctaC
Sequence domains:
Structure domains:

Ligands and Environments

11 bound ligands:
Ligand DMU 9 x DMU
Ligand CU 6 x CU
Ligand MG 2 x MG
Ligand CA 2 x CA
Ligand OH 2 x OH
Ligand PO4 2 x PO4
Ligand HEA 4 x HEA
Ligand TRD 23 x TRD
Ligand CD 5 x CD
Ligand HTO 1 x HTO
Ligand DXC 1 x DXC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P212121
Unit cell:
a: 123.243Å b: 132.052Å c: 167.966Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.184 0.212
Expression system: Cereibacter sphaeroides

Quick links

Citations

6 review citations

Highlighting membrane protein structure and function: A celebration of the Protein Data Bank.
Li et al. (2021)
5 more

10 mentions without citation

Gating and regulation of the cytochrome c oxidase proton pump.
Ferguson-Miller et al. (2012)
9 more