› 2wdv

X-ray diffraction
3.2Å resolution

E. coli succinate:quinone oxidoreductase (SQR) with an empty quinone- binding pocket

Released:
DOI: 10.2210/pdb2wdv/pdb
PDB entry 2wdv coloured by chain, front view.
PDB entry 2wdv coloured by chain, side view.
PDB entry 2wdv coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.
Ruprecht J, Yankovskaya V, Maklashina E, Iwata S, Cecchini G
J Biol Chem 284 29836-46 (2009)
PMID: 19710024

Function and Biology Details

Reaction catalysed: 
Succinate + a quinone = fumarate + a quinol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139344 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Succinate dehydrogenase flavoprotein subunit Chains: A, E, I
Molecule details ›
Chains: A, E, I
Length: 588 amino acids
Theoretical weight: 64.5 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AC41 (Residues: 1-588; Coverage: 100%)
Gene names: JW0713, b0723, sdhA
Sequence domains:
Structure domains:
Succinate dehydrogenase iron-sulfur subunit Chains: B, F, J
Molecule details ›
Chains: B, F, J
Length: 238 amino acids
Theoretical weight: 26.8 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P07014 (Residues: 1-238; Coverage: 100%)
Gene names: JW0714, b0724, sdhB
Sequence domains:
Structure domains:
Succinate dehydrogenase cytochrome b556 subunit Chains: C, G, K
Molecule details ›
Chains: C, G, K
Length: 129 amino acids
Theoretical weight: 14.31 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P69054 (Residues: 1-129; Coverage: 100%)
Gene names: JW0711, b0721, cybA, sdhC
Sequence domains: Succinate dehydrogenase/Fumarate reductase transmembrane subunit
Structure domains: Fumarate reductase/succinate dehydrogenase, transmembrane subunit
Succinate dehydrogenase hydrophobic membrane anchor subunit Chains: D, H, L
Molecule details ›
Chains: D, H, L
Length: 115 amino acids
Theoretical weight: 12.87 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AC44 (Residues: 1-115; Coverage: 100%)
Gene names: JW0712, b0722, sdhD
Sequence domains: Succinate dehydrogenase/Fumarate reductase transmembrane subunit
Structure domains: Fumarate reductase/succinate dehydrogenase, transmembrane subunit

Ligands and Environments


Cofactor: Ligand FAD 3 x FAD

Cofactor: Ligand HEM 3 x HEM
5 bound ligands:
Ligand TEO 3 x TEO
Ligand NA 3 x NA
Ligand FES 3 x FES
Ligand SF4 3 x SF4
Ligand F3S 3 x F3S
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 120.34Å b: 184.847Å c: 204.72Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.205 0.233
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Differential effects of complex II on mitochondrial ROS production and their relation to cardioprotective pre- and postconditioning.
Dröse S. (2013)
13 more

4 mentions without citation

Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.
Ruprecht et al. (2009)
3 more