› 5yjy

X-ray diffraction
3.4Å resolution

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with AC0-12.

Released:
DOI: 10.2210/pdb5yjy/pdb
PDB entry 5yjy coloured by chain, front view.
PDB entry 5yjy coloured by chain, side view.
PDB entry 5yjy coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors.
Yamashita T, Inaoka DK, Shiba T, Oohashi T, Iwata S, Yagi T, Kosaka H, Miyoshi H, Harada S, Kita K, Hirano K
Sci Rep 8 2427 (2018)
PMID: 29402945

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152271 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 485 amino acids
Theoretical weight: 54.13 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P32340 (Residues: 29-513; Coverage: 95%)
Gene names: NDI1, YM7056.06C, YML120C
Sequence domains: Pyridine nucleotide-disulphide oxidoreductase
Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 486 amino acids
Theoretical weight: 54.24 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P32340 (Residues: 28-513; Coverage: 95%)
Gene names: NDI1, YM7056.06C, YML120C
Sequence domains: Pyridine nucleotide-disulphide oxidoreductase

Ligands and Environments


Cofactor: Ligand FAD 2 x FAD
3 bound ligands:
Ligand MG 8 x MG
Ligand 8WF 2 x 8WF
Ligand MES 2 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 69.854Å b: 115.795Å c: 166.499Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.207 0.299
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Thriving in Oxygen While Preventing ROS Overproduction: No Two Systems Are Created Equal.
Mendez-Romero et al. (2022)
7 other articles

2 mentions without citation

Structure of the NDH-2 - HQNO inhibited complex provides molecular insight into quinone-binding site inhibitors.
Petri et al. (2018)
1 more