4pd4

X-ray diffraction
3.04Å resolution

Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 22-mer (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 S288C
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 S288C
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: 43.69 KDa
Source organism: Saccharomyces cerevisiae S288C
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 S288C
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 S288C
UniProt:
  • Canonical: P08067 (Residues: 31-215; Coverage: 86%)
Gene names: RIP1, YEL024W
Sequence domains: Rieske [2Fe-2S] domain
Structure domains:
Cytochrome b-c1 complex subunit 6, mitochondrial Chain: F
Molecule details ›
Chain: F
Length: 74 amino acids
Theoretical weight: 8.85 KDa
Source organism: Saccharomyces cerevisiae S288C
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: G
Molecule details ›
Chain: G
Length: 126 amino acids
Theoretical weight: 14.45 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chain: H
Molecule details ›
Chain: H
Length: 93 amino acids
Theoretical weight: 10.86 KDa
Source organism: Saccharomyces cerevisiae S288C
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 Chain: I
Molecule details ›
Chain: I
Length: 57 amino acids
Theoretical weight: 6.54 KDa
Source organism: Saccharomyces cerevisiae S288C
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
Ig-like domain-containing protein Chain: J
Molecule details ›
Chain: J
Length: 127 amino acids
Theoretical weight: 14.37 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q53VQ5 (Residues: 1-119; Coverage: 98%)
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins
Ig kappa chain V-V region HP 124E1 Chain: K
Molecule details ›
Chain: K
Length: 107 amino acids
Theoretical weight: 11.93 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01647 (Residues: 1-107; Coverage: 99%)
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments


Cofactor: Ligand UQ6 1 x UQ6

Cofactor: Ligand HEM 3 x HEM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2
Unit cell:
a: 212.26Å b: 150.88Å c: 143.09Å
α: 90° β: 115.18° γ: 90°
R-values:
R R work R free
0.269 0.268 0.297
Expression system: Escherichia coli