› 6rfq

Electron Microscopy
3.3Å resolution

Cryo-EM structure of a respiratory complex I assembly intermediate with NDUFAF2

Released:
DOI: 10.2210/pdb6rfq/pdb
PDB entry 6rfq coloured by chain, front view.
PDB entry 6rfq coloured by chain, side view.
PDB entry 6rfq coloured by chain, top view.
Source organism: Yarrowia lipolytica
Primary publication:
High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease.
Parey K, Haapanen O, Sharma V, Köfeler H, Züllig T, Prinz S, Siegmund K, Wittig I, Mills DJ, Vonck J, Kühlbrandt W, Zickermann V
Sci Adv 5 eaax9484 (2019)
PMID: 31844670
Related structures: EMD-4872

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 41-mer (preferred)
PDBe Complex ID:
PDB-CPX-103385 (preferred)
Entry contents:
41 distinct polypeptide molecules
Macromolecules (41 distinct):
YALI0D05467p Chain: A
Molecule details ›
Chain: A
Length: 728 amino acids
Theoretical weight: 79.09 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: F2Z6F1 (Residues: 1-728; Coverage: 100%)
Gene name: YALI0_D05467g
Sequence domains:
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 488 amino acids
Theoretical weight: 53.83 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: F2Z660 (Residues: 1-488; Coverage: 100%)
Gene name: YALI0_B20372g
Sequence domains:
NADH-quinone oxidoreductase subunit D domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 466 amino acids
Theoretical weight: 52.49 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: F2Z626 (Residues: 1-466; Coverage: 100%)
Gene name: YALI0_F17248g
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: D
Molecule details ›
Chain: D
Length: 87 amino acids
Theoretical weight: 9.81 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: B5FVD3 (Residues: 1-87; Coverage: 100%)
Gene name: YALI0_C21789g
Sequence domains: NADH-ubiquinone oxidoreductase MWFE subunit
NAD-dependent epimerase/dehydratase domain-containing protein Chain: E
Molecule details ›
Chain: E
Length: 375 amino acids
Theoretical weight: 42.77 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C7X4 (Residues: 1-375; Coverage: 100%)
Gene name: YALI0_D24585g
Sequence domains: NAD dependent epimerase/dehydratase family
ETC complex I subunit conserved region-domain-containing protein Chain: F
Molecule details ›
Chain: F
Length: 144 amino acids
Theoretical weight: 16.66 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C4W9 (Residues: 1-144; Coverage: 100%)
Gene name: YALI0_E23089g
Sequence domains: ETC complex I subunit conserved region
NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein Chain: G
Molecule details ›
Chain: G
Length: 281 amino acids
Theoretical weight: 32.39 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: F2Z6D7 (Residues: 1-281; Coverage: 100%)
Gene name: YALI0_F02123g
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
YALI0D00737p Chain: H
Molecule details ›
Chain: H
Length: 243 amino acids
Theoretical weight: 27.25 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: F2Z6C0 (Residues: 1-243; Coverage: 100%)
Gene name: YALI0_D00737g
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
4Fe-4S ferredoxin-type domain-containing protein Chain: I
Molecule details ›
Chain: I
Length: 229 amino acids
Theoretical weight: 25.68 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: F2Z619 (Residues: 1-229; Coverage: 100%)
Gene name: YALI0_F00924g
Sequence domains: 4Fe-4S dicluster domain
YALI0E11891p Chain: J
Molecule details ›
Chain: J
Length: 198 amino acids
Theoretical weight: 20.85 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C674 (Residues: 1-198; Coverage: 100%)
Gene name: YALI0_E11891g
NADH:ubiquinone oxidoreductase-like 20kDa subunit domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 210 amino acids
Theoretical weight: 23.46 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C2Q1 (Residues: 1-173; Coverage: 80%)
Gene name: YALI0_F06050g
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
Acyl carrier protein Chain: O
Molecule details ›
Chain: O
Length: 109 amino acids
Theoretical weight: 12.05 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C926 (Residues: 1-109; Coverage: 100%)
Gene name: YALI0_D14850g
Sequence domains: Phosphopantetheine attachment site
Complex 1 LYR protein domain-containing protein Chain: P
Molecule details ›
Chain: P
Length: 124 amino acids
Theoretical weight: 14.78 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6CI60 (Residues: 1-124; Coverage: 100%)
Gene name: YALI0_A01419g
Sequence domains: Complex1_LYR-like
Acyl carrier protein Chain: Q
Molecule details ›
Chain: Q
Length: 132 amino acids
Theoretical weight: 14.44 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C7X2 (Residues: 1-132; Coverage: 100%)
Gene name: YALI0_D24629g
Sequence domains: Phosphopantetheine attachment site
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: R
Molecule details ›
Chain: R
Length: 109 amino acids
Theoretical weight: 12.9 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C9Z1 (Residues: 1-109; Coverage: 100%)
Gene name: YALI0_D07216g
NUWM protein Chain: S
Molecule details ›
Chain: S
Length: 249 amino acids
Theoretical weight: 28.48 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: F2Z673 (Residues: 1-249; Coverage: 100%)
Gene name: YALI0_E29095g
NADH-ubiquinone oxidoreductase Chain: U
Molecule details ›
Chain: U
Length: 172 amino acids
Theoretical weight: 19.36 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6CGB4 (Residues: 1-172; Coverage: 100%)
Gene name: YALI0_A20680g
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: W
Molecule details ›
Chain: W
Length: 123 amino acids
Theoretical weight: 14.11 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: B5FVF8 (Residues: 1-123; Coverage: 100%)
Gene name: YALI0_E28930g
Sequence domains: GRIM-19 protein
NADH-ubiquinone oxidoreductase 21 kDa subunit Chain: X
Molecule details ›
Chain: X
Length: 169 amino acids
Theoretical weight: 18.59 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C4A6 (Residues: 1-169; Coverage: 100%)
Gene name: YALI0_E28424g
Sequence domains:
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: Y
Molecule details ›
Chain: Y
Length: 161 amino acids
Theoretical weight: 18.66 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6CEK9 (Residues: 1-161; Coverage: 100%)
Gene name: YALI0_B14861g
Sequence domains: NADH dehydrogenase ubiquinone Fe-S protein 4
NADH-ubiquinone oxidoreductase 21.3 kDa subunit Chain: Z
Molecule details ›
Chain: Z
Length: 182 amino acids
Theoretical weight: 19.77 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6CI10 (Residues: 1-182; Coverage: 100%)
Gene name: YALI0_A02651g
YALI0D04939p Chain: a
Molecule details ›
Chain: a
Length: 149 amino acids
Theoretical weight: 17.33 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6CA88 (Residues: 1-149; Coverage: 100%)
Gene name: YALI0_D04939g
Sequence domains: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8)
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I) Chain: b
Molecule details ›
Chain: b
Length: 74 amino acids
Theoretical weight: 8.06 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: A0A1D8NGI5 (Residues: 1-74; Coverage: 100%)
Gene name: YALI1_E00527g
NADH-ubiquinone oxidoreductase B12 subunit family-domain-containing protein Chain: c
Molecule details ›
Chain: c
Length: 60 amino acids
Theoretical weight: 6.95 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: B5FVE5 (Residues: 1-60; Coverage: 100%)
Gene name: YALI0_D10274g
Sequence domains: NADH-ubiquinone oxidoreductase B12 subunit family
NADH-ubiquinone oxidoreductase 12 kDa subunit Chain: d
Molecule details ›
Chain: d
Length: 92 amino acids
Theoretical weight: 11.04 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: B5RSK3 (Residues: 1-92; Coverage: 100%)
Gene name: YALI0_A17946g
Sequence domains: NADH-ubiquinone oxidoreductase subunit 10
Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I) Chain: e
Molecule details ›
Chain: e
Length: 67 amino acids
Theoretical weight: 7.81 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: A0A1D8NFX6 (Residues: 1-67; Coverage: 100%)
Gene names: B0I71DRAFT_129560, YALI1_D30003g
Ribosomal protein/NADH dehydrogenase domain-containing protein Chain: f
Molecule details ›
Chain: f
Length: 87 amino acids
Theoretical weight: 9.62 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6CD73 (Residues: 1-87; Coverage: 100%)
Gene name: YALI0_C03201g
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
NADH-ubiquinone oxidoreductase 9.5 kDa subunit Chain: g
Molecule details ›
Chain: g
Length: 78 amino acids
Theoretical weight: 8.92 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: B5FVF3 (Residues: 1-78; Coverage: 100%)
Gene name: YALI0_E23749g
Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I) Chain: i
Molecule details ›
Chain: i
Length: 90 amino acids
Theoretical weight: 9.79 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: A0A1H6Q311 (Residues: 1-90; Coverage: 100%)
Gene names: B0I71DRAFT_133979, YALI1_D22691g
NADH-ubiquinone oxidoreductase B15 subunit Chain: j
Molecule details ›
Chain: j
Length: 93 amino acids
Theoretical weight: 10.49 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: B5RSK9 (Residues: 1-93; Coverage: 100%)
Gene name: YALI0_F06061g
NADH-ubiquinone oxidoreductase assembly factor N7BML Chain: k
Molecule details ›
Chain: k
Length: 237 amino acids
Theoretical weight: 27.65 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C7L6 (Residues: 1-237; Coverage: 100%)
Gene names: N7BML, YALI0D27082g
Sequence domains: NADH ubiquinone oxidoreductase subunit NDUFA12
YALI0F14003p Chain: n
Molecule details ›
Chain: n
Length: 120 amino acids
Theoretical weight: 13.52 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q6C1R9 (Residues: 20-139; Coverage: 86%)
Gene name: YALI0_F14003g
NADH-ubiquinone oxidoreductase chain 1 Chain: 1
Molecule details ›
Chain: 1
Length: 341 amino acids
Theoretical weight: 38.36 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6E8 (Residues: 1-341; Coverage: 100%)
Gene name: ND1
Sequence domains: NADH dehydrogenase
NADH-ubiquinone oxidoreductase chain 2 Chain: 2
Molecule details ›
Chain: 2
Length: 469 amino acids
Theoretical weight: 53.35 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6C8 (Residues: 1-469; Coverage: 100%)
Gene name: ND2
Sequence domains: Proton-conducting membrane transporter
NADH-ubiquinone oxidoreductase chain 3 Chain: 3
Molecule details ›
Chain: 3
Length: 128 amino acids
Theoretical weight: 14.48 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6C7 (Residues: 1-128; Coverage: 100%)
Gene name: ND3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH-ubiquinone oxidoreductase chain 4 Chain: 4
Molecule details ›
Chain: 4
Length: 486 amino acids
Theoretical weight: 54.51 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6D6 (Residues: 1-486; Coverage: 100%)
Gene name: ND4
Sequence domains: Proton-conducting membrane transporter
NADH-ubiquinone oxidoreductase chain 5 Chain: 5
Molecule details ›
Chain: 5
Length: 655 amino acids
Theoretical weight: 73.74 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: Q9B6D3 (Residues: 1-655; Coverage: 100%)
Gene name: ND5
Sequence domains:
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
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: 8
Molecule details ›
Chain: 8
Length: 99 amino acids
Theoretical weight: 11.22 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: B5FVG1 (Residues: 1-99; Coverage: 100%)
Gene name: YALI0_E31766g
Sequence domains: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7)
YALI0F18359p Chain: 9
Molecule details ›
Chain: 9
Length: 89 amino acids
Theoretical weight: 10.04 KDa
Source organism: Yarrowia lipolytica
UniProt:
  • Canonical: B5RSL7 (Residues: 1-89; Coverage: 100%)
Gene name: YALI0_F18359g
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa

Ligands and Environments


Cofactor: Ligand FMN 1 x FMN

Cofactor: Ligand NDP 1 x NDP
9 bound ligands:
Ligand SF4 6 x SF4
Ligand FES 2 x FES
Ligand 3PE 10 x 3PE
Ligand LMN 2 x LMN
Ligand CDL 4 x CDL
Ligand ZMP 2 x ZMP
Ligand PLC 4 x PLC
Ligand T7X 3 x T7X
Ligand CPL 1 x CPL
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-4872

Quick links

Citations

13 review citations

Mitochondrial Metabolism as a Target for Cancer Therapy.
Vasan et al. (2020)
12 more

3 mentions without citation

Accessory Subunits of the Matrix Arm of Mitochondrial Complex I with a Focus on Subunit NDUFS4 and Its Role in Complex I Function and Assembly.
Kahlhöfer et al. (2021)
2 more