› 3aee

X-ray diffraction
3.22Å resolution

Crystal structure of porcine heart mitochondrial complex II bound with Atpenin A5

Released:
DOI: 10.2210/pdb3aee/pdb
PDB entry 3aee coloured by chain, front view.
PDB entry 3aee coloured by chain, side view.
PDB entry 3aee coloured by chain, top view.
Source organism: Sus scrofa
Entry authors: Harada S, Sasaki T, Shindo M, Kido Y, Inaoka DK, Omori J, Osanai A, Sakamoto K, Mao J, Matsuoka S, Inoue M, Honma T, Tanaka A, Kita K

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-107594 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 622 amino acids
Theoretical weight: 68.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q0QF01 (Residues: 43-664; Coverage: 94%)
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: 28.76 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q007T0 (Residues: 29-280; Coverage: 90%)
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: 15.3 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: D0VWV4 (Residues: 30-169; Coverage: 83%)
Gene name: SDHC
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: 10.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A5GZW8 (Residues: 57-159; Coverage: 65%)
Gene name: SDHD
Sequence domains: CybS, succinate dehydrogenase cytochrome B small subunit
Structure domains: Fumarate reductase/succinate dehydrogenase, transmembrane subunit

Ligands and Environments


Cofactor: Ligand AT5 1 x AT5

Cofactor: Ligand FAD 1 x FAD

Cofactor: Ligand HEM 1 x HEM
3 bound ligands:
Ligand FES 1 x FES
Ligand F3S 1 x F3S
Ligand SF4 1 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P212121
Unit cell:
a: 70.751Å b: 83.841Å c: 293.735Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.232 0.282

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