› 4u3f

X-ray diffraction
3.23Å resolution

Cytochrome bc1 complex from chicken with designed inhibitor bound

Released:
DOI: 10.2210/pdb4u3f/pdb
PDB entry 4u3f coloured by chain, front view.
PDB entry 4u3f coloured by chain, side view.
PDB entry 4u3f coloured by chain, top view.
Source organism: Gallus gallus
Primary publication:
Rational Design of Highly Potent and Slow-Binding Cytochrome Inhibitor as Fungicide by Computational Substitution Optimization.
Hao G, Yang S, Huang W, Wang L, Shen Y, Tu W, Li H, Huang L, Wu J, Berry EA, Yang G.
Sci Rep 5 (2015)

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 analysis Details

Assembly composition:
hetero icosamer (preferred)
PDBe Complex ID:
PDB-CPX-236840 (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: 42.65 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: P18946 (Residues: 2-380; Coverage: 100%)
Gene names: COB, CYTB, MT-CYB, MTCYB
Sequence domains:
Structure domains: Cytochrome Bc1 Complex; Chain C
Cytochrome c domain-containing protein Chains: D, Q
Molecule details ›
Chains: D, Q
Length: 241 amino acids
Theoretical weight: 26.97 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: D0VX26 (Residues: 1-241; Coverage: 100%)
Sequence domains: Cytochrome C1 family
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: 76 amino acids
Theoretical weight: 7.72 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: Q5ZLR5 (Residues: 2-76; Coverage: 28%)
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: F1NC51 (Residues: 2-62; Coverage: 98%)
Gene name: UQCR10
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 14 x PEE
Ligand Y52 2 x Y52
Ligand U10 2 x U10
Ligand MES 1 x MES
Ligand GOL 2 x GOL
Ligand CDL 4 x CDL
Ligand BOG 3 x BOG
Ligand FES 2 x FES
1 modified residue:
Ligand FME 2 x FME

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P212121
Unit cell:
a: 167.251Å b: 181.483Å c: 239.631Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.236 0.284

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