› 2ibz

X-ray diffraction
2.3Å resolution

Yeast Cytochrome BC1 Complex with Stigmatellin

Released:
DOI: 10.2210/pdb2ibz/pdb
PDB entry 2ibz coloured by chain, front view.
PDB entry 2ibz coloured by chain, side view.
PDB entry 2ibz coloured by chain, top view.
Source organisms:
Primary publication:
A comparison of stigmatellin conformations, free and bound to the photosynthetic reaction center and the cytochrome bc1 complex.
Lancaster CR, Hunte C, Kelley J, Trumpower BL, Ditchfield R
J Mol Biol 368 197-208 (2007)
PMID: 17337272

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 undecamer (preferred)
PDBe Complex ID:
PDB-CPX-106138 (preferred)
Entry contents:
11 distinct polypeptide molecules
Macromolecules (11 distinct):
Cytochrome b-c1 complex subunit 1, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 431 amino acids
Theoretical weight: 47.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07256 (Residues: 27-457; Coverage: 94%)
Gene names: COR1, QCR1, YBL0403, YBL045C
Sequence domains:
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
Cytochrome b-c1 complex subunit 2, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 352 amino acids
Theoretical weight: 38.75 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07257 (Residues: 17-368; Coverage: 96%)
Gene names: COR2, P9677.6, QCR2, UCR2, YPR191W
Sequence domains: Insulinase (Peptidase family M16)
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
Cytochrome b Chain: C
Molecule details ›
Chain: C
Length: 385 amino acids
Theoretical weight: 43.67 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00163 (Residues: 1-385; Coverage: 100%)
Gene names: COB, CYTB, Q0105
Sequence domains:
Structure domains: Cytochrome Bc1 Complex; Chain C
Cytochrome c1, heme protein, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 248 amino acids
Theoretical weight: 27.81 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07143 (Residues: 62-309; Coverage: 80%)
Gene names: CTC1, CYT1, YOR065W, YOR29-16
Sequence domains: Cytochrome C1 family
Structure domains:
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chain: E
Molecule details ›
Chain: E
Length: 185 amino acids
Theoretical weight: 20.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P08067 (Residues: 31-215; Coverage: 86%)
Gene names: RIP1, YEL024W
Sequence domains:
Structure domains:
Cytochrome b-c1 complex subunit 6, mitochondrial Chain: H
Molecule details ›
Chain: H
Length: 74 amino acids
Theoretical weight: 8.85 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00127 (Residues: 74-147; Coverage: 50%)
Gene names: QCR6, UCR6, YFR033C
Sequence domains: Ubiquinol-cytochrome C reductase hinge protein
Structure domains: Ubiquinol-cytochrome C reductase hinge domain
Cytochrome b-c1 complex subunit 7, mitochondrial Chain: F
Molecule details ›
Chain: F
Length: 127 amino acids
Theoretical weight: 14.58 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00128 (Residues: 1-127; Coverage: 100%)
Gene names: CRO1, D9719.32, QCR7, UCR7, YDR529C
Sequence domains: Ubiquinol-cytochrome C reductase complex 14kD subunit
Structure domains: Cytochrome b-c1 complex subunit 7
Cytochrome b-c1 complex subunit 8, mitochondrial Chain: G
Molecule details ›
Chain: G
Length: 94 amino acids
Theoretical weight: 10.99 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P08525 (Residues: 1-94; Coverage: 100%)
Gene names: J0526, QCR8, YJL166W
Sequence domains: UcrQ family
Structure domains: Cytochrome b-c1 complex subunit 8
Cytochrome b-c1 complex subunit 9, mitochondrial Chain: I
Molecule details ›
Chain: I
Length: 66 amino acids
Theoretical weight: 7.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22289 (Residues: 1-66; Coverage: 100%)
Gene names: QCR9, UCR9, YGR183C
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
Structure domains: Cytochrome b-c1 complex subunit 9
Ig heavy chain V region 3-6 Chain: X
Molecule details ›
Chain: X
Length: 127 amino acids
Theoretical weight: 14.37 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P18531 (Residues: 19-116; Coverage: 100%)
Gene names: Gm16932, Ighv3-6
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chain: Y
Molecule details ›
Chain: Y
Length: 107 amino acids
Theoretical weight: 11.93 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: A0N6Y3 (Residues: 1-107; Coverage: 100%)
Gene name: Ig VL
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments


Cofactor: Ligand HEC 3 x HEC

Cofactor: Ligand UQ6 1 x UQ6
2 bound ligands:
Ligand SMA 1 x SMA
Ligand FES 1 x FES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: C2
Unit cell:
a: 214.473Å b: 163.921Å c: 147.276Å
α: 90° β: 117.5° γ: 90°
R-values:
R R work R free
0.222 0.222 0.256
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes.
Sarewicz et al. (2021)
4 more

9 mentions without citation

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