› 6q9b

Electron Microscopy
3.9Å resolution

CI Membrane Arm focused refinement from Ovine respiratory SC I+III2

Released:
DOI: 10.2210/pdb6q9b/pdb
PDB entry 6q9b coloured by chain, front view.
PDB entry 6q9b coloured by chain, side view.
PDB entry 6q9b coloured by chain, top view.
Source organism: Ovis aries
Primary publication:
Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.
Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA
Mol Cell 75 1131-1146.e6 (2019)
PMID: 31492636
Related structures: EMD-4479

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 29-mer (preferred)
PDBe Complex ID:
PDB-CPX-131280 (preferred)
Entry contents:
29 distinct polypeptide molecules
Macromolecules (29 distinct):
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chain: S2
Molecule details ›
Chain: S2
Length: 430 amino acids
Theoretical weight: 49.19 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PJ73 (Residues: 1-412; Coverage: 100%)
Gene name: NDUFS2
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NADH-ubiquinone oxidoreductase chain 3 Chain: D3
Molecule details ›
Chain: D3
Length: 115 amino acids
Theoretical weight: 13.11 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: O78753 (Residues: 1-115; Coverage: 100%)
Gene names: MT-ND3, MTND3, NADH3, ND3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH-ubiquinone oxidoreductase chain 1 Chain: D1
Molecule details ›
Chain: D1
Length: 318 amino acids
Theoretical weight: 35.88 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: O78747 (Residues: 1-318; Coverage: 100%)
Gene names: MT-ND1, MTND1, NADH1, ND1
Sequence domains: NADH dehydrogenase
NADH-ubiquinone oxidoreductase chain 6 Chain: D6
Molecule details ›
Chain: D6
Length: 175 amino acids
Theoretical weight: 19.13 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: O78757 (Residues: 1-175; Coverage: 100%)
Gene names: MT-ND6, MTND6, NADH6, ND6
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NADH-ubiquinone oxidoreductase chain 4L Chain: 4L
Molecule details ›
Chain: 4L
Length: 98 amino acids
Theoretical weight: 10.84 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: O78754 (Residues: 1-98; Coverage: 100%)
Gene names: MT-ND4L, MTND4L, NADH4L, ND4L
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
NADH-ubiquinone oxidoreductase chain 5 Chain: D5
Molecule details ›
Chain: D5
Length: 606 amino acids
Theoretical weight: 68.41 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: O78756 (Residues: 1-606; Coverage: 100%)
Gene names: MT-ND5, MTND5, NADH5, ND5
Sequence domains:
NADH-ubiquinone oxidoreductase chain 4 Chain: D4
Molecule details ›
Chain: D4
Length: 459 amino acids
Theoretical weight: 52.06 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: O78755 (Residues: 1-459; Coverage: 100%)
Gene names: MT-ND4, MTND4, NADH4, ND4
Sequence domains:
NADH-ubiquinone oxidoreductase chain 2 Chain: D2
Molecule details ›
Chain: D2
Length: 347 amino acids
Theoretical weight: 39.15 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: O78748 (Residues: 1-347; Coverage: 100%)
Gene names: MT-ND2, MTND2, NADH2, ND2
Sequence domains:
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chain: AK
Molecule details ›
Chain: AK
Length: 140 amino acids
Theoretical weight: 14.61 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit B5 Chain: B5
Molecule details ›
Chain: B5
Length: 143 amino acids
Theoretical weight: 16.71 KDa
Source organism: Ovis aries
Acyl carrier protein Chain: AB
Molecule details ›
Chain: AB
Length: 88 amino acids
Theoretical weight: 10.12 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5NQT7 (Residues: 70-157; Coverage: 56%)
Sequence domains: Phosphopantetheine attachment site
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: A8
Molecule details ›
Chain: A8
Length: 171 amino acids
Theoretical weight: 20.01 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit B10 Chain: BJ
Molecule details ›
Chain: BJ
Length: 175 amino acids
Theoretical weight: 20.88 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chain: AJ
Molecule details ›
Chain: AJ
Length: 320 amino acids
Theoretical weight: 36.8 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit S5 Chain: S5
Molecule details ›
Chain: S5
Length: 105 amino acids
Theoretical weight: 12.47 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit A3 Chain: A3
Molecule details ›
Chain: A3
Length: 83 amino acids
Theoretical weight: 9.19 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit B3 Chain: B3
Molecule details ›
Chain: B3
Length: 97 amino acids
Theoretical weight: 11.02 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chain: C2
Molecule details ›
Chain: C2
Length: 120 amino acids
Theoretical weight: 14.23 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5P9Q8 (Residues: 3-122; Coverage: 98%)
Gene name: NDUFC2
Sequence domains: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Chain: B4
Molecule details ›
Chain: B4
Length: 128 amino acids
Theoretical weight: 14.98 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5QF73 (Residues: 3-130; Coverage: 99%)
Gene name: NDUFB4
Sequence domains: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: AM
Molecule details ›
Chain: AM
Length: 143 amino acids
Theoretical weight: 16.64 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 Chain: B6
Molecule details ›
Chain: B6
Length: 127 amino acids
Theoretical weight: 15.43 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PZE3 (Residues: 2-128; Coverage: 99%)
Gene name: NDUFB6
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit
NADH:ubiquinone oxidoreductase subunit B7 Chain: B7
Molecule details ›
Chain: B7
Length: 136 amino acids
Theoretical weight: 16.28 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit B9 Chain: B9
Molecule details ›
Chain: B9
Length: 178 amino acids
Theoretical weight: 21.65 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit B2 Chain: B2
Molecule details ›
Chain: B2
Length: 72 amino acids
Theoretical weight: 8.5 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: B8
Molecule details ›
Chain: B8
Length: 158 amino acids
Theoretical weight: 18.82 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5Q1B0 (Residues: 29-186; Coverage: 85%)
Gene name: NDUFB8
Sequence domains: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial Chain: BK
Molecule details ›
Chain: BK
Length: 125 amino acids
Theoretical weight: 14.46 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial Chain: C1
Molecule details ›
Chain: C1
Length: 49 amino acids
Theoretical weight: 5.81 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 Chain: B1
Molecule details ›
Chain: B1
Length: 57 amino acids
Theoretical weight: 6.93 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5QG39 (Residues: 2-58; Coverage: 98%)
Gene name: LOC114115567
Sequence domains: MNLL subunit
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: A1
Molecule details ›
Chain: A1
Length: 70 amino acids
Theoretical weight: 8.21 KDa
Source organism: Ovis aries

Ligands and Environments

4 bound ligands:
Ligand 3PE 6 x 3PE
Ligand CDL 4 x CDL
Ligand PC1 2 x PC1
Ligand ZMP 1 x ZMP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-4479

Quick links

Citations

23 review citations

Generation of Reactive Oxygen Species by Mitochondria.
Hernansanz-Agustín et al. (2021)
22 more

2 mentions without citation

Atomic structure of a mitochondrial complex I intermediate from vascular plants.
Maldonado et al. (2020)
1 more