› 4gav

X-ray diffraction
3Å resolution

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with quinone

Released:
DOI: 10.2210/pdb4gav/pdb
Model geometry
Fit model/data
PDB entry 4gav coloured by chain, front view.
PDB entry 4gav coloured by chain, side view.
PDB entry 4gav coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
The structure of the yeast NADH dehydrogenase (Ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates.
Iwata M, Lee Y, Yamashita T, Yagi T, Iwata S, Cameron AD, Maher MJ
Proc Natl Acad Sci U S A 109 15247-52 (2012)
PMID: 22949654

Function and Biology Details

Reaction catalysed: 
NADH + a quinone = NAD(+) + a quinol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152272 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 471 amino acids
Theoretical weight: 52.8 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P32340 (Residues: 43-513; Coverage: 92%)
Gene names: NDI1, YM7056.06C, YML120C
Sequence domains:
Structure domains: FAD/NAD(P)-binding domain

Ligands and Environments


Cofactor: Ligand FAD 2 x FAD
1 bound ligand:
Ligand UQ2 2 x UQ2
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 65.589Å b: 111.926Å c: 165.525Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.241 0.24 0.268
Expression system: Escherichia coli

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Citations

9 review citations

Energetics of Respiration and Oxidative Phosphorylation in Mycobacteria.
Cook et al. (2014)
8 more

2 mentions without citation

The structure of the yeast NADH dehydrogenase (Ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates.
Iwata et al. (2012)
1 more