› 2h89

X-ray diffraction
2.4Å resolution

Avian Respiratory Complex II with Malonate Bound

Released:
DOI: 10.2210/pdb2h89/pdb
PDB entry 2h89 coloured by chain, front view.
PDB entry 2h89 coloured by chain, side view.
PDB entry 2h89 coloured by chain, top view.
Source organism: Gallus gallus
Primary publication:
Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state.
Huang LS, Shen JT, Wang AC, Berry EA
Biochim Biophys Acta 1757 1073-83
PMID: 16935256

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)
PDBe Complex ID:
PDB-CPX-112133 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 621 amino acids
Theoretical weight: 68.26 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: Q9YHT1 (Residues: 45-665; Coverage: 93%)
Gene name: SDHA
Sequence domains:
Structure domains:
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 252 amino acids
Theoretical weight: 28.69 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: Q9YHT2 (Residues: 39-290; Coverage: 87%)
Gene name: SDHB
Sequence domains:
Structure domains:
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial Chain: C
Molecule details ›
Chain: C
Length: 140 amino acids
Theoretical weight: 15.39 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: D0VWW3 (Residues: 1-140; Coverage: 100%)
Sequence domains: Succinate dehydrogenase/Fumarate reductase transmembrane subunit
Structure domains:
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 103 amino acids
Theoretical weight: 10.97 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: Q5ZIS0 (Residues: 55-157; Coverage: 66%)
Gene names: RCJMB04_23p7, SDHD
Sequence domains: CybS, succinate dehydrogenase cytochrome B small subunit
Structure domains: Fumarate reductase/succinate dehydrogenase, transmembrane subunit

Ligands and Environments


Cofactor: Ligand HEM 1 x HEM

Cofactor: Ligand FAD 1 x FAD
8 bound ligands:
Ligand K 2 x K
Ligand MLI 1 x MLI
Ligand UNL 40 x UNL
Ligand FES 1 x FES
Ligand SF4 1 x SF4
Ligand F3S 1 x F3S
Ligand BHG 1 x BHG
Ligand PEE 2 x PEE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 70.52Å b: 84.118Å c: 292.212Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.226 0.279

Quick links

Citations

7 review citations

Review: studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with bis-histidine and histidine-methionine axial iron coordination.
Zoppellaro et al. (2009)
6 more

6 mentions without citation

Succinate dehydrogenase is a direct target of sirtuin 3 deacetylase activity.
Finley et al. (2011)
5 more