› 6h8k

X-ray diffraction
3.79Å resolution

Crystal structure of a variant (Q133C in PSST) of Yarrowia lipolytica complex I

Released:
DOI: 10.2210/pdb6h8k/pdb
PDB entry 6h8k coloured by chain, front view.
PDB entry 6h8k coloured by chain, side view.
PDB entry 6h8k coloured by chain, top view.
Source organism: Yarrowia lipolytica
Primary publication:
Locking loop movement in the ubiquinone pocket of complex I disengages the proton pumps.
Cabrera-Orefice A, Yoga EG, Wirth C, Siegmund K, Zwicker K, Guerrero-Castillo S, Zickermann V, Hunte C, Brandt U
Nat Commun 9 4500 (2018)
PMID: 30374105

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 73-mer (preferred)
PDBe Complex ID:
PDB-CPX-166813 (preferred)
Entry contents:
48 distinct polypeptide molecules
Macromolecules (48 distinct):
NADH-ubiquinone oxidoreductase chain 1 Chain: 1
Molecule details ›
Chain: 1
Length: 335 amino acids
Theoretical weight: 37.7 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6E8 (Residues: 1-335; Coverage: 98%)
Gene name: ND1
Sequence domains: NADH dehydrogenase
NADH-ubiquinone oxidoreductase chain 2 Chain: 2
Molecule details ›
Chain: 2
Length: 434 amino acids
Theoretical weight: 46.37 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6C8 (Residues: 1-415; Coverage: 84%)
Gene name: ND2
Sequence domains: Proton-conducting membrane transporter
NADH-ubiquinone oxidoreductase chain 3 Chain: 3
Molecule details ›
Chain: 3
Length: 110 amino acids
Theoretical weight: 12.35 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6C7 (Residues: 1-110; Coverage: 86%)
Gene name: ND3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH-ubiquinone oxidoreductase chain 4 Chain: 4
Molecule details ›
Chain: 4
Length: 470 amino acids
Theoretical weight: 46.53 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6D6 (Residues: 136-471; Coverage: 69%)
Gene name: ND4
Sequence domains: Proton-conducting membrane transporter
NADH-ubiquinone oxidoreductase chain 5 Chain: 5
Molecule details ›
Chain: 5
Length: 616 amino acids
Theoretical weight: 61.4 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6D3 (Residues: 73-653; Coverage: 83%)
Gene name: ND5
Sequence domains:
NADH-ubiquinone oxidoreductase chain 6 Chain: 6
Molecule details ›
Chain: 6
Length: 184 amino acids
Theoretical weight: 20.18 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6E9 (Residues: 11-185; Coverage: 95%)
Gene name: ND6
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NUAM protein Chain: A
Molecule details ›
Chain: A
Length: 634 amino acids
Theoretical weight: 56.42 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9UUU3 (Residues: 69-199; Coverage: 17%)
Gene names: B0I71DRAFT_14167, YALI1_D07089g, nuam
Sequence domains:
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 370 amino acids
Theoretical weight: 34.32 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9UUU2 (Residues: 92-434; Coverage: 61%)
Gene names: NUO51, YALI1_B26679g, nubm
Sequence domains:
NADH-quinone oxidoreductase subunit D domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 383 amino acids
Theoretical weight: 43.26 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9UUU1 (Residues: 83-465; Coverage: 82%)
Gene names: B0I71DRAFT_131656, YALI1_F22993g, nucm
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NUEM protein Chain: E
Molecule details ›
Chain: E
Length: 195 amino acids
Theoretical weight: 16.61 KDa
Source organism: Yarrowia lipolytica
NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein Chain: G
Molecule details ›
Chain: G
Length: 133 amino acids
Theoretical weight: 13.5 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9UUU0 (Residues: 69-209; Coverage: 47%)
Gene names: B0I71DRAFT_126141, nugm
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I) Chain: H
Molecule details ›
Chain: H
Length: 154 amino acids
Theoretical weight: 13.3 KDa
Source organism: Yarrowia lipolytica
4Fe-4S ferredoxin-type domain-containing protein Chain: I
Molecule details ›
Chain: I
Length: 140 amino acids
Theoretical weight: 14.43 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9UUT8 (Residues: 72-196; Coverage: 47%)
Gene names: B0I71DRAFT_132693, YALI1_F01456g, nuim
Sequence domains: 4Fe-4S dicluster domain
NADH:ubiquinone oxidoreductase-like 20kDa subunit domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 147 amino acids
Theoretical weight: 16.51 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9UUT7 (Residues: 59-205; Coverage: 70%)
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: 79 amino acids
Theoretical weight: 8.74 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6D4 (Residues: 1-79; Coverage: 89%)
Gene name: ND4L
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
Unknown polypeptide Chains: Z, r
Molecule details ›
Chains: Z, r
Length: 17 amino acids
Theoretical weight: 1.46 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: AF, Y
Molecule details ›
Chains: AF, Y
Length: 40 amino acids
Theoretical weight: 3.42 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: U
Molecule details ›
Chain: U
Length: 10 amino acids
Theoretical weight: 869 Da
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: X
Molecule details ›
Chain: X
Length: 57 amino acids
Theoretical weight: 4.87 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: W
Molecule details ›
Chain: W
Length: 54 amino acids
Theoretical weight: 4.61 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: V
Molecule details ›
Chain: V
Length: 63 amino acids
Theoretical weight: 5.38 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: AI, T, m
Molecule details ›
Chains: AI, T, m
Length: 20 amino acids
Theoretical weight: 1.72 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: AJ, AL, S
Molecule details ›
Chains: AJ, AL, S
Length: 19 amino acids
Theoretical weight: 1.64 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: R
Molecule details ›
Chain: R
Length: 50 amino acids
Theoretical weight: 4.27 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: Q
Molecule details ›
Chain: Q
Length: 70 amino acids
Theoretical weight: 5.98 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: P
Molecule details ›
Chain: P
Length: 28 amino acids
Theoretical weight: 2.4 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: AC, AH, AM, F, f
Molecule details ›
Chains: AC, AH, AM, F, f
Length: 18 amino acids
Theoretical weight: 1.55 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: O, l
Molecule details ›
Chains: O, l
Length: 25 amino acids
Theoretical weight: 2.15 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: M
Molecule details ›
Chain: M
Length: 51 amino acids
Theoretical weight: 4.36 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: D
Molecule details ›
Chain: D
Length: 30 amino acids
Theoretical weight: 2.57 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: J
Molecule details ›
Chain: J
Length: 69 amino acids
Theoretical weight: 5.89 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: N
Molecule details ›
Chain: N
Length: 15 amino acids
Theoretical weight: 1.29 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: a, i
Molecule details ›
Chains: a, i
Length: 26 amino acids
Theoretical weight: 2.23 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: b
Molecule details ›
Chain: b
Length: 22 amino acids
Theoretical weight: 1.89 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: AE, AK, AO, c, g
Molecule details ›
Chains: AE, AK, AO, c, g
Length: 9 amino acids
Theoretical weight: 784 Da
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: AB, AN, d, o
Molecule details ›
Chains: AB, AN, d, o
Length: 16 amino acids
Theoretical weight: 1.38 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: e, w, z
Molecule details ›
Chains: e, w, z
Length: 13 amino acids
Theoretical weight: 1.12 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: h
Molecule details ›
Chain: h
Length: 47 amino acids
Theoretical weight: 4.02 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: j
Molecule details ›
Chain: j
Length: 48 amino acids
Theoretical weight: 4.1 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: k, s
Molecule details ›
Chains: k, s
Length: 23 amino acids
Theoretical weight: 1.98 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: n, q
Molecule details ›
Chains: n, q
Length: 36 amino acids
Theoretical weight: 3.08 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: p
Molecule details ›
Chain: p
Length: 76 amino acids
Theoretical weight: 6.49 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: t
Molecule details ›
Chain: t
Length: 45 amino acids
Theoretical weight: 3.85 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: u
Molecule details ›
Chain: u
Length: 32 amino acids
Theoretical weight: 2.74 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: v, y
Molecule details ›
Chains: v, y
Length: 11 amino acids
Theoretical weight: 954 Da
Source organism: Yarrowia lipolytica
Unknown polypeptide Chains: AG, x
Molecule details ›
Chains: AG, x
Length: 8 amino acids
Theoretical weight: 699 Da
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: AA
Molecule details ›
Chain: AA
Length: 58 amino acids
Theoretical weight: 4.95 KDa
Source organism: Yarrowia lipolytica
Unknown polypeptide Chain: AD
Molecule details ›
Chain: AD
Length: 39 amino acids
Theoretical weight: 3.34 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: 316.31Å b: 316.31Å c: 819.18Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.361 0.361 0.363

Quick links

Citations

7 review citations

Mitochondrial Structure and Bioenergetics in Normal and Disease Conditions.
Protasoni et al. (2021)
6 more

2 mentions without citation

Spatial arrangement of proteins in planar and curved membranes by PPM 3.0.
Lomize et al. (2022)
1 more