› 6xvf

X-ray diffraction
3.5Å resolution

Crystal structure of bovine cytochrome bc1 in complex with tetrahydro-quinolone inhibitor JAG021

Released:
DOI: 10.2210/pdb6xvf/pdb
PDB entry 6xvf coloured by chain, front view.
PDB entry 6xvf coloured by chain, side view.
PDB entry 6xvf coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Potent Tetrahydroquinolone Eliminates Apicomplexan Parasites.
McPhillie MJ, Zhou Y, Hickman MR, Gordon JA, Weber CR, Li Q, Lee PJ, Amporndanai K, Johnson RM, Darby H, Woods S, Li ZH, Priestley RS, Ristroph KD, Biering SB, El Bissati K, Hwang S, Hakim FE, Dovgin SM, Lykins JD, Roberts L, Hargrave K, Cong H, Sinai AP, Muench SP, Dubey JP, Prud'homme RK, Lorenzi HA, Biagini GA, Moreno SN, Roberts CW, Antonyuk SV, Fishwick CWG, McLeod R
Front Cell Infect Microbiol 10 203 (2020)
PMID: 32626661

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-132265 (preferred)
Entry contents:
10 distinct polypeptide molecules
Macromolecules (10 distinct):
Cytochrome b-c1 complex subunit 1, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 445 amino acids
Theoretical weight: 49.17 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P31800 (Residues: 36-480; Coverage: 93%)
Gene name: UQCRC1
Sequence domains:
Cytochrome b-c1 complex subunit 2, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 418 amino acids
Theoretical weight: 44.5 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P23004 (Residues: 36-453; Coverage: 92%)
Gene name: UQCRC2
Sequence domains:
Cytochrome b Chain: C
Molecule details ›
Chain: C
Length: 378 amino acids
Theoretical weight: 42.49 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00157 (Residues: 2-379; Coverage: 100%)
Gene names: COB, CYTB, MT-CYB, MTCYB
Sequence domains:
Cytochrome c1, heme protein, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 239 amino acids
Theoretical weight: 27.11 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00125 (Residues: 86-324; Coverage: 74%)
Gene name: CYC1
Sequence domains: Cytochrome C1 family
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chain: E
Molecule details ›
Chain: E
Length: 196 amino acids
Theoretical weight: 21.64 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13272 (Residues: 79-274; Coverage: 72%)
Gene name: UQCRFS1
Sequence domains:
Cytochrome b-c1 complex subunit 7 Chain: F
Molecule details ›
Chain: F
Length: 100 amino acids
Theoretical weight: 12.49 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00129 (Residues: 12-111; Coverage: 90%)
Gene name: UQCRB
Sequence domains: Ubiquinol-cytochrome C reductase complex 14kD subunit
Cytochrome b-c1 complex subunit 8 Chain: G
Molecule details ›
Chain: G
Length: 74 amino acids
Theoretical weight: 8.8 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13271 (Residues: 3-76; Coverage: 90%)
Gene name: UQCRQ
Sequence domains: UcrQ family
Cytochrome b-c1 complex subunit 6, mitochondrial Chain: H
Molecule details ›
Chain: H
Length: 64 amino acids
Theoretical weight: 7.52 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00126 (Residues: 27-90; Coverage: 70%)
Gene name: UQCRH
Sequence domains: Ubiquinol-cytochrome C reductase hinge protein
Cytochrome b-c1 complex subunit 9 Chain: I
Molecule details ›
Chain: I
Length: 46 amino acids
Theoretical weight: 4.83 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13272 (Residues: 33-78; Coverage: 17%)
Gene name: UQCRFS1
Sequence domains: Ubiquinol-cytochrome c reductase 8 kDa, N-terminal
Cytochrome b-c1 complex subunit 9 Chain: J
Molecule details ›
Chain: J
Length: 59 amino acids
Theoretical weight: 6.87 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00130 (Residues: 3-61; Coverage: 92%)
Gene name: UQCR10
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like

Ligands and Environments

11 bound ligands:
Ligand PG4 3 x PG4
Ligand 6PE 1 x 6PE
Ligand PO4 9 x PO4
Ligand CDL 4 x CDL
Ligand HEM 2 x HEM
Ligand LMT 1 x LMT
Ligand PEE 2 x PEE
Ligand JAG 1 x JAG
Ligand HEC 1 x HEC
Ligand FES 1 x FES
Ligand PX4 1 x PX4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P6522
Unit cell:
a: 209.869Å b: 209.869Å c: 342.418Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.218 0.217 0.232

Quick links

Citations

5 review citations

Toxoplasma gondii infection and its implications within the central nervous system.
Matta et al. (2021)
4 more

1 mention without citation

Potent Tetrahydroquinolone Eliminates Apicomplexan Parasites.
McPhillie et al. (2020)