› 1kyo

X-ray diffraction
2.97Å resolution

YEAST CYTOCHROME BC1 COMPLEX WITH BOUND SUBSTRATE CYTOCHROME C

Released:
DOI: 10.2210/pdb1kyo/pdb
PDB entry 1kyo coloured by chain, front view.
PDB entry 1kyo coloured by chain, side view.
PDB entry 1kyo coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c.
Lange C, Hunte C
Proc Natl Acad Sci U S A 99 2800-5 (2002)
PMID: 11880631

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 23-mer (preferred)
PDBe Complex ID:
PDB-CPX-226690 (preferred)
Entry contents:
12 distinct polypeptide molecules
Macromolecules (12 distinct):
Cytochrome b-c1 complex subunit 1, mitochondrial Chains: A, L
Molecule details ›
Chains: A, L
Length: 430 amino acids
Theoretical weight: 47.36 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 Chains: B, M
Molecule details ›
Chains: B, M
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 Chains: C, N
Molecule details ›
Chains: C, N
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 Chains: D, O
Molecule details ›
Chains: D, O
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 Chains: E, P
Molecule details ›
Chains: E, P
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 Chains: F, Q
Molecule details ›
Chains: F, Q
Length: 74 amino acids
Theoretical weight: 8.87 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 Chains: G, R
Molecule details ›
Chains: G, R
Length: 126 amino acids
Theoretical weight: 14.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00128 (Residues: 2-127; Coverage: 99%)
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 Chains: H, S
Molecule details ›
Chains: H, S
Length: 93 amino acids
Theoretical weight: 10.86 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P08525 (Residues: 2-94; Coverage: 99%)
Gene names: J0526, QCR8, YJL166W
Sequence domains: UcrQ family
Structure domains: Cytochrome b-c1 complex subunit 8
Cytochrome b-c1 complex subunit 9, mitochondrial Chains: I, T
Molecule details ›
Chains: I, T
Length: 57 amino acids
Theoretical weight: 6.51 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22289 (Residues: 2-58; Coverage: 86%)
Gene names: QCR9, UCR9, YGR183C
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
Structure domains: Cytochrome b-c1 complex subunit 9
HEAVY CHAIN (VH) OF FV-FRAGMENT Chains: J, U
Molecule details ›
Chains: J, U
Length: 127 amino acids
Theoretical weight: 14.37 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins
LIGHT CHAIN (VL) OF FV-FRAGMENT Chains: K, V
Molecule details ›
Chains: K, V
Length: 107 amino acids
Theoretical weight: 11.93 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Cytochrome c isoform 1 Chain: W
Molecule details ›
Chain: W
Length: 108 amino acids
Theoretical weight: 12.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00044 (Residues: 2-109; Coverage: 99%)
Gene names: CYC1, J1653, YJR048W
Sequence domains: Cytochrome c
Structure domains: Cytochrome c-like domain

Ligands and Environments


Cofactor: Ligand HEC 7 x HEC
2 bound ligands:
Ligand SMA 2 x SMA
Ligand FES 2 x FES
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P21
Unit cell:
a: 147.224Å b: 165.531Å c: 195.889Å
α: 90° β: 104.19° γ: 90°
R-values:
R R work R free
0.229 0.229 0.268
Expression system: Escherichia coli

Quick links

Citations

45 review citations

The multiple functions of cytochrome c and their regulation in life and death decisions of the mammalian cell: From respiration to apoptosis.
Hüttemann et al. (2011)
44 more

29 mentions without citation

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