› 6zkr

Electron Microscopy
3.5Å resolution

Native complex I, open3

Released:
DOI: 10.2210/pdb6zkr/pdb
PDB entry 6zkr coloured by chain, front view.
PDB entry 6zkr coloured by chain, side view.
PDB entry 6zkr coloured by chain, top view.
Source organism: Ovis aries
Primary publication:
The coupling mechanism of mammalian respiratory complex I.
Kampjut D, Sazanov LA
Science 370 (2020)
PMID: 32972993
Related structures: EMD-11259

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 45-mer (preferred)
PDBe Complex ID:
PDB-CPX-131306 (preferred)
Entry contents:
44 distinct polypeptide molecules
Macromolecules (44 distinct):
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: 1
Molecule details ›
Chain: 1
Length: 464 amino acids
Theoretical weight: 50.69 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PUX0 (Residues: 1-464; Coverage: 100%)
Gene name: NDUFV1
Sequence domains:
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: 2
Molecule details ›
Chain: 2
Length: 246 amino acids
Theoretical weight: 27.37 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5NRY1 (Residues: 1-246; Coverage: 100%)
Gene name: NDUFV2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH:ubiquinone oxidoreductase core subunit S1 Chain: 3
Molecule details ›
Chain: 3
Length: 727 amino acids
Theoretical weight: 79.52 KDa
Source organism: Ovis aries
Mitochondrial complex I, 49 kDa subunit Chain: 4
Molecule details ›
Chain: 4
Length: 463 amino acids
Theoretical weight: 52.66 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial Chain: 5
Molecule details ›
Chain: 5
Length: 266 amino acids
Theoretical weight: 30.38 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PB27 (Residues: 1-266; Coverage: 100%)
Gene name: NDUFS3
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
Mitochondrial complex I, PSST subunit Chain: 6
Molecule details ›
Chain: 6
Length: 223 amino acids
Theoretical weight: 24.62 KDa
Source organism: Ovis aries
Mitochondrial complex I, TYKY subunit Chain: 9
Molecule details ›
Chain: 9
Length: 217 amino acids
Theoretical weight: 24.5 KDa
Source organism: Ovis aries
NADH-ubiquinone oxidoreductase chain 3 Chain: A
Molecule details ›
Chain: A
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: H
Molecule details ›
Chain: H
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: J
Molecule details ›
Chain: J
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: K
Molecule details ›
Chain: K
Length: 98 amino acids
Theoretical weight: 10.87 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: L
Molecule details ›
Chain: L
Length: 606 amino acids
Theoretical weight: 68.44 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: M
Molecule details ›
Chain: M
Length: 459 amino acids
Theoretical weight: 52.09 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: N
Molecule details ›
Chain: N
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:
Mitochondrial complex I, B14.7 subunit Chain: V
Molecule details ›
Chain: V
Length: 141 amino acids
Theoretical weight: 14.78 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit B5 Chain: W
Molecule details ›
Chain: W
Length: 189 amino acids
Theoretical weight: 21.61 KDa
Source organism: Ovis aries
Acyl carrier protein Chains: X, j
Molecule details ›
Chains: X, j
Length: 157 amino acids
Theoretical weight: 17.61 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5NQT7 (Residues: 1-157; Coverage: 100%)
Sequence domains: Phosphopantetheine attachment site
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: Y
Molecule details ›
Chain: Y
Length: 172 amino acids
Theoretical weight: 20.14 KDa
Source organism: Ovis aries
Mitochondrial complex I, PDSW subunit Chain: Z
Molecule details ›
Chain: Z
Length: 175 amino acids
Theoretical weight: 20.88 KDa
Source organism: Ovis aries
Mitochondrial complex I, 10 kDa subunit Chain: a
Molecule details ›
Chain: a
Length: 109 amino acids
Theoretical weight: 11.92 KDa
Source organism: Ovis aries
Mitochondrial complex I, 13 kDa subunit Chain: b
Molecule details ›
Chain: b
Length: 124 amino acids
Theoretical weight: 13.46 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 170 amino acids
Theoretical weight: 19.38 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PE07 (Residues: 1-170; Coverage: 100%)
Gene name: NDUFS4
Sequence domains: NADH dehydrogenase ubiquinone Fe-S protein 4
NADH:ubiquinone oxidoreductase subunit A9 Chain: d
Molecule details ›
Chain: d
Length: 380 amino acids
Theoretical weight: 43.03 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: e
Molecule details ›
Chain: e
Length: 99 amino acids
Theoretical weight: 11.1 KDa
Source organism: Ovis aries
Mitochondrial complex I, B13 subunit Chain: f
Molecule details ›
Chain: f
Length: 116 amino acids
Theoretical weight: 13.29 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: g
Molecule details ›
Chain: g
Length: 140 amino acids
Theoretical weight: 16.3 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5QC06 (Residues: 1-140; Coverage: 100%)
Gene name: NDUFA6
Sequence domains: Complex 1 protein (LYR family)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 Chain: h
Molecule details ›
Chain: h
Length: 114 amino acids
Theoretical weight: 12.7 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5P0I2 (Residues: 1-114; Coverage: 100%)
Gene name: NDUFA7
Sequence domains: NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Chain: i
Molecule details ›
Chain: i
Length: 145 amino acids
Theoretical weight: 17.12 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chain: k
Molecule details ›
Chain: k
Length: 355 amino acids
Theoretical weight: 40.56 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit S5 Chain: l
Molecule details ›
Chain: l
Length: 106 amino acids
Theoretical weight: 12.61 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit A3 Chain: m
Molecule details ›
Chain: m
Length: 84 amino acids
Theoretical weight: 9.33 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit B3 Chain: n
Molecule details ›
Chain: n
Length: 98 amino acids
Theoretical weight: 11.15 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chain: o
Molecule details ›
Chain: o
Length: 122 amino acids
Theoretical weight: 14.43 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5P9Q8 (Residues: 1-122; Coverage: 100%)
Gene name: NDUFC2
Sequence domains: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Chain: p
Molecule details ›
Chain: p
Length: 130 amino acids
Theoretical weight: 15.24 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5QF73 (Residues: 1-130; Coverage: 100%)
Gene name: NDUFB4
Sequence domains: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4)
Mitochondrial complex I, B16.6 subunit Chain: q
Molecule details ›
Chain: q
Length: 144 amino acids
Theoretical weight: 16.77 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 Chain: r
Molecule details ›
Chain: r
Length: 128 amino acids
Theoretical weight: 15.57 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PZE3 (Residues: 1-128; Coverage: 100%)
Gene name: NDUFB6
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit
NADH:ubiquinone oxidoreductase subunit B7 Chain: s
Molecule details ›
Chain: s
Length: 137 amino acids
Theoretical weight: 16.41 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit B9 Chain: t
Molecule details ›
Chain: t
Length: 179 amino acids
Theoretical weight: 21.78 KDa
Source organism: Ovis aries
NADH:ubiquinone oxidoreductase subunit B2 Chain: u
Molecule details ›
Chain: u
Length: 108 amino acids
Theoretical weight: 12.23 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: v
Molecule details ›
Chain: v
Length: 186 amino acids
Theoretical weight: 21.75 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5Q1B0 (Residues: 1-186; Coverage: 100%)
Gene name: NDUFB8
Sequence domains: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8)
Mitochondrial complex I, ESSS subunit Chain: w
Molecule details ›
Chain: w
Length: 154 amino acids
Theoretical weight: 17.41 KDa
Source organism: Ovis aries
Mitochondrial complex I, KFYI subunit Chain: x
Molecule details ›
Chain: x
Length: 76 amino acids
Theoretical weight: 8.8 KDa
Source organism: Ovis aries
Mitochondrial complex I, MNLL subunit Chain: y
Molecule details ›
Chain: y
Length: 58 amino acids
Theoretical weight: 7.08 KDa
Source organism: Ovis aries
Mitochondrial complex I, MWFE subunit Chain: z
Molecule details ›
Chain: z
Length: 70 amino acids
Theoretical weight: 8.21 KDa
Source organism: Ovis aries

Ligands and Environments

12 bound ligands:
Ligand SF4 6 x SF4
Ligand FMN 1 x FMN
Ligand FES 2 x FES
Ligand K 1 x K
Ligand PC1 6 x PC1
Ligand 3PE 14 x 3PE
Ligand CDL 8 x CDL
Ligand ZMP 2 x ZMP
Ligand ZN 1 x ZN
Ligand NDP 1 x NDP
Ligand AMP 1 x AMP
Ligand MYR 1 x MYR
4 modified residues:
Ligand 2MR 1 x 2MR
Ligand FME 3 x FME
Ligand AYA 2 x AYA
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-11259

Quick links

Citations

23 review citations

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

1 mention without citation

Analysis of Human Mutations in the Supernumerary Subunits of Complex I.
Dang et al. (2020)