› 3cwb

X-ray diffraction
3.51Å resolution

Chicken Cytochrome BC1 Complex inhibited by an iodinated analogue of the polyketide Crocacin-D

Released:
DOI: 10.2210/pdb3cwb/pdb
PDB entry 3cwb coloured by chain, front view.
PDB entry 3cwb coloured by chain, side view.
PDB entry 3cwb coloured by chain, top view.
Source organism: Gallus gallus
Primary publication:
The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D.
Crowley PJ, Berry EA, Cromartie T, Daldal F, Godfrey CR, Lee DW, Phillips JE, Taylor A, Viner R
Bioorg Med Chem 16 10345-55 (2008)
PMID: 18996700

Function and Biology Details

Reaction catalysed: 
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
PDBe Complex ID:
PDB-CPX-112211 (preferred)
Entry contents:
10 distinct polypeptide molecules
Macromolecules (10 distinct):
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i Chains: A, N
Molecule details ›
Chains: A, N
Length: 446 amino acids
Theoretical weight: 49.5 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: D0VX31 (Residues: 1-446; Coverage: 100%)
Sequence domains:
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2 Chains: B, O
Molecule details ›
Chains: B, O
Length: 441 amino acids
Theoretical weight: 46.68 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: D0VX29 (Residues: 1-441; Coverage: 100%)
Sequence domains:
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
Cytochrome b Chains: C, P
Molecule details ›
Chains: C, P
Length: 380 amino acids
Theoretical weight: 42.62 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: P18946 (Residues: 1-380; Coverage: 100%)
Gene names: COB, CYTB, MT-CYB, MTCYB
Sequence domains:
Structure domains: Cytochrome Bc1 Complex; Chain C
MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN Chains: D, Q
Molecule details ›
Chains: D, Q
Length: 241 amino acids
Theoretical weight: 26.97 KDa
Source organism: Gallus gallus
Structure domains:
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: E, R
Molecule details ›
Chains: E, R
Length: 196 amino acids
Theoretical weight: 21.51 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: Q5ZLR5 (Residues: 77-272; Coverage: 72%)
Gene names: RCJMB04_5b19, UQCRFS1
Sequence domains:
Structure domains:
Cytochrome b-c1 complex subunit 7 Chains: F, S
Molecule details ›
Chains: F, S
Length: 110 amino acids
Theoretical weight: 13.39 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: D0VX30 (Residues: 1-110; Coverage: 100%)
Sequence domains: Ubiquinol-cytochrome C reductase complex 14kD subunit
Structure domains: Cytochrome b-c1 complex subunit 7
Cytochrome b-c1 complex subunit 8 Chains: G, T
Molecule details ›
Chains: G, T
Length: 81 amino acids
Theoretical weight: 9.5 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: D0VX32 (Residues: 1-81; Coverage: 100%)
Sequence domains: UcrQ family
Structure domains: Cytochrome b-c1 complex subunit 8
Cytochrome b-c1 complex subunit 6 Chains: H, U
Molecule details ›
Chains: H, U
Length: 77 amino acids
Theoretical weight: 9.06 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: D0VX28 (Residues: 1-77; Coverage: 100%)
Sequence domains: Ubiquinol-cytochrome C reductase hinge protein
Structure domains: Ubiquinol-cytochrome C reductase hinge domain
Cytochrome b-c1 complex subunit 9 Chains: I, V
Molecule details ›
Chains: I, V
Length: 52 amino acids
Theoretical weight: 5.21 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: Q5ZLR5 (Residues: 45-76; Coverage: 12%)
Gene names: RCJMB04_5b19, UQCRFS1
Sequence domains: Ubiquinol-cytochrome c reductase 8 kDa, N-terminal
Structure domains: Cytochrome Bc1 Complex; Chain I
Complex III subunit 9 Chains: J, W
Molecule details ›
Chains: J, W
Length: 61 amino acids
Theoretical weight: 7.01 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: D0VX27 (Residues: 1-61; Coverage: 100%)
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
Structure domains: Cytochrome b-c1 complex subunit 9

Ligands and Environments


Cofactor: Ligand HEC 2 x HEC

Cofactor: Ligand HEM 4 x HEM
8 bound ligands:
Ligand PEE 6 x PEE
Ligand BOG 6 x BOG
Ligand AZI 2 x AZI
Ligand ICX 2 x ICX
Ligand UQ 2 x UQ
Ligand CDL 4 x CDL
Ligand FES 2 x FES
Ligand UNL 4 x UNL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P212121
Unit cell:
a: 174.778Å b: 182.663Å c: 242.945Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.285 0.285 0.319

Quick links

Citations

8 review citations

Myxobacterial secondary metabolites: bioactivities and modes-of-action.
Weissman et al. (2010)
7 more

11 mentions without citation

Structural analysis of cytochrome bc1 complexes: implications to the mechanism of function.
Xia et al. (2013)
10 more