› 3fyi

X-ray diffraction
2.2Å resolution

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides in the reduced state bound with cyanide

Released:
DOI: 10.2210/pdb3fyi/pdb
PDB 3fyi coloured by chain and viewed from the front.
PDB 3fyi coloured by chain and viewed from the side.
PDB 3fyi coloured by chain and viewed from the top.
Source organism: Rhodobacter sphaeroides
Primary publication:
Redox-dependent conformational changes in cytochrome C oxidase suggest a gating mechanism for proton uptake.
Qin L, Liu J, Mills DA, Proshlyakov DA, Hiser C, Ferguson-Miller S
Biochemistry 48 5121-30 (2009)
PMID: 19397279

Function and Biology Details

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

Structure analysis Details

Assembly composition:
Non-polymer only dimer (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: Rhodobacter sphaeroides
Expression system: Rhodobacter 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: Rhodobacter sphaeroides
Expression system: Rhodobacter sphaeroides
UniProt:
  • Canonical: Q03736 (Residues: 26-281; Coverage: 92%)
Gene names: coxII, ctaB, ctaC
Sequence domains:
Structure domains:

Ligands and Environments

9 bound ligands:
Ligand HEA 4 x HEA
Ligand CU1 6 x CU1
Ligand MG 2 x MG
Ligand CA 2 x CA
Ligand CYN 2 x CYN
Ligand DMU 10 x DMU
Ligand TRD 12 x TRD
Ligand HTO 1 x HTO
Ligand CD 4 x CD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P212121
Unit cell:
a: 124.344Å b: 131.877Å c: 176.16Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.194 0.219
Expression system: Rhodobacter sphaeroides

Quick links

Citations

13 review citations

Oxygen Activation and Energy Conservation by Cytochrome c Oxidase.
Wikström et al. (2018)
12 more

2 mentions without citation

Redox-dependent conformational changes in cytochrome C oxidase suggest a gating mechanism for proton uptake.
Qin et al. (2009)
1 more