› 4wz7

X-ray diffraction
3.6Å resolution

Crystal structure of mitochondrial NADH:ubiquinone oxidoreductase from Yarrowia lipolytica.

Released:
DOI: 10.2210/pdb4wz7/pdb
PDB entry 4wz7 coloured by chain, front view.
PDB entry 4wz7 coloured by chain, side view.
PDB entry 4wz7 coloured by chain, top view.
Source organism: Yarrowia lipolytica
Primary publication:
Structural biology. Mechanistic insight from the crystal structure of mitochondrial complex I.
Zickermann V, Wirth C, Nasiri H, Siegmund K, Schwalbe H, Hunte C, Brandt U
Science 347 44-9 (2015)
PMID: 25554780

Function and Biology Details

Reaction catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 67-mer (preferred)
PDBe Complex ID:
PDB-CPX-165336 (preferred)
Entry contents:
48 distinct polypeptide molecules
Macromolecules (48 distinct):
NADH-ubiquinone oxidoreductase chain 1 Chain: 1
Molecule details ›
Chain: 1
Length: 327 amino acids
Theoretical weight: 33.59 KDa
Source organism: Yarrowia lipolytica
NADH dehydrogenase subunit 2 Chain: 2
Molecule details ›
Chain: 2
Length: 438 amino acids
Theoretical weight: 46.16 KDa
Source organism: Yarrowia lipolytica
NADH-ubiquinone oxidoreductase chain 3 Chain: 3
Molecule details ›
Chain: 3
Length: 89 amino acids
Theoretical weight: 9.39 KDa
Source organism: Yarrowia lipolytica
NADH-ubiquinone oxidoreductase chain 4 Chain: 4
Molecule details ›
Chain: 4
Length: 470 amino acids
Theoretical weight: 46.08 KDa
Source organism: Yarrowia lipolytica
NADH-ubiquinone oxidoreductase chain 5 Chain: 5
Molecule details ›
Chain: 5
Length: 619 amino acids
Theoretical weight: 61.82 KDa
Source organism: Yarrowia lipolytica
NADH-ubiquinone oxidoreductase chain 6 Chain: 6
Molecule details ›
Chain: 6
Length: 185 amino acids
Theoretical weight: 20.77 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6E9 (Residues: 1-185; Coverage: 100%)
Gene name: ND6
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NUAM protein Chain: A
Molecule details ›
Chain: A
Length: 628 amino acids
Theoretical weight: 54.07 KDa
Source organism: Yarrowia lipolytica
NUBM protein Chain: B
Molecule details ›
Chain: B
Length: 370 amino acids
Theoretical weight: 33.14 KDa
Source organism: Yarrowia lipolytica
NUCM protein Chain: C
Molecule details ›
Chain: C
Length: 444 amino acids
Theoretical weight: 49.82 KDa
Source organism: Yarrowia lipolytica
39-kDa subunit Chain: E
Molecule details ›
Chain: E
Length: 195 amino acids
Theoretical weight: 16.61 KDa
Source organism: Yarrowia lipolytica
NUGM protein Chain: G
Molecule details ›
Chain: G
Length: 133 amino acids
Theoretical weight: 13.44 KDa
Source organism: Yarrowia lipolytica
Subunit NUHM of protein NADH:Ubiquinone Oxidoreductase (Complex I) Chain: H
Molecule details ›
Chain: H
Length: 154 amino acids
Theoretical weight: 13.29 KDa
Source organism: Yarrowia lipolytica
Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I) Chain: I
Molecule details ›
Chain: I
Length: 137 amino acids
Theoretical weight: 13.36 KDa
Source organism: Yarrowia lipolytica
NADH:ubiquinone oxidoreductase-like 20kDa subunit domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 183 amino acids
Theoretical weight: 20.45 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9UUT7 (Residues: 28-210; Coverage: 87%)
Gene names: B0I71DRAFT_136033, YALI1_F09003g, nukm
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH-ubiquinone oxidoreductase chain 4L Chain: L
Molecule details ›
Chain: L
Length: 89 amino acids
Theoretical weight: 9.82 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6D4 (Residues: 1-89; Coverage: 100%)
Gene name: ND4L
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
unknown subunits 1 Chains: D, Z
Molecule details ›
Chains: D, Z
Length: 57 amino acids
Theoretical weight: 4.87 KDa
Source organism: Yarrowia lipolytica
unknown subunits 2 Chain: F
Molecule details ›
Chain: F
Length: 54 amino acids
Theoretical weight: 4.61 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: J
Molecule details ›
Chain: J
Length: 63 amino acids
Theoretical weight: 5.38 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: M
Molecule details ›
Chain: M
Length: 29 amino acids
Theoretical weight: 2.49 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: N
Molecule details ›
Chain: N
Length: 50 amino acids
Theoretical weight: 4.27 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: O
Molecule details ›
Chain: O
Length: 70 amino acids
Theoretical weight: 5.98 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: P
Molecule details ›
Chain: P
Length: 46 amino acids
Theoretical weight: 3.93 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: Q
Molecule details ›
Chain: Q
Length: 51 amino acids
Theoretical weight: 4.36 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: R
Molecule details ›
Chain: R
Length: 30 amino acids
Theoretical weight: 2.57 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: S
Molecule details ›
Chain: S
Length: 69 amino acids
Theoretical weight: 5.89 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chains: AH, T
Molecule details ›
Chains: AH, T
Length: 15 amino acids
Theoretical weight: 1.29 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: U
Molecule details ›
Chain: U
Length: 26 amino acids
Theoretical weight: 2.23 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: V
Molecule details ›
Chain: V
Length: 22 amino acids
Theoretical weight: 1.89 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chains: AB, AY, BE, W
Molecule details ›
Chains: AB, AY, BE, W
Length: 9 amino acids
Theoretical weight: 784 Da
Source organism: Yarrowia lipolytica
unknown subunits Chains: AJ, AV, BH, X
Molecule details ›
Chains: AJ, AV, BH, X
Length: 16 amino acids
Theoretical weight: 1.38 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chains: AR, AT, Y
Molecule details ›
Chains: AR, AT, Y
Length: 13 amino acids
Theoretical weight: 1.12 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chains: AA, AW, BB, BG
Molecule details ›
Chains: AA, AW, BB, BG
Length: 18 amino acids
Theoretical weight: 1.55 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chains: AC, AD
Molecule details ›
Chains: AC, AD
Length: 47 amino acids
Theoretical weight: 4.02 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: AE
Molecule details ›
Chain: AE
Length: 48 amino acids
Theoretical weight: 4.1 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: AF
Molecule details ›
Chain: AF
Length: 35 amino acids
Theoretical weight: 3 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: AG
Molecule details ›
Chain: AG
Length: 25 amino acids
Theoretical weight: 2.15 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chains: AI, AL
Molecule details ›
Chains: AI, AL
Length: 36 amino acids
Theoretical weight: 3.08 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chains: AK, AN
Molecule details ›
Chains: AK, AN
Length: 76 amino acids
Theoretical weight: 6.49 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: AM
Molecule details ›
Chain: AM
Length: 17 amino acids
Theoretical weight: 1.46 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: AO
Molecule details ›
Chain: AO
Length: 32 amino acids
Theoretical weight: 2.74 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chains: AP, AS
Molecule details ›
Chains: AP, AS
Length: 11 amino acids
Theoretical weight: 954 Da
Source organism: Yarrowia lipolytica
unknown subunits Chains: AQ, BA
Molecule details ›
Chains: AQ, BA
Length: 8 amino acids
Theoretical weight: 699 Da
Source organism: Yarrowia lipolytica
unknown subunits Chain: AU
Molecule details ›
Chain: AU
Length: 58 amino acids
Theoretical weight: 4.95 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: AX
Molecule details ›
Chain: AX
Length: 39 amino acids
Theoretical weight: 3.34 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: AZ
Molecule details ›
Chain: AZ
Length: 40 amino acids
Theoretical weight: 3.42 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: BC
Molecule details ›
Chain: BC
Length: 20 amino acids
Theoretical weight: 1.72 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chains: BD, BF
Molecule details ›
Chains: BD, BF
Length: 19 amino acids
Theoretical weight: 1.64 KDa
Source organism: Yarrowia lipolytica
unknown subunits Chain: BI
Molecule details ›
Chain: BI
Length: 905 amino acids
Theoretical weight: 77.04 KDa
Source organism: Yarrowia lipolytica

Ligands and Environments

2 bound ligands:
Ligand FES 2 x FES
Ligand SF4 6 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: R32
Unit cell:
a: 317.74Å b: 317.74Å c: 818.97Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.317 0.316 0.341

Quick links

Citations

50 review citations

A Unifying Mechanism for Mitochondrial Superoxide Production during Ischemia-Reperfusion Injury.
Chouchani et al. (2016)
49 more

12 mentions without citation

Ischemic A/D transition of mitochondrial complex I and its role in ROS generation.
Dröse et al. (2016)
11 more