› 7zdh

Electron Microscopy
3.46Å resolution

Complex I from Ovis aries at pH7.4, Closed state

Released:
DOI: 10.2210/pdb7zdh/pdb
PDB entry 7zdh coloured by chain, front view.
PDB entry 7zdh coloured by chain, side view.
PDB entry 7zdh coloured by chain, top view.
Source organism: Ovis aries
Primary publication:
A universal coupling mechanism of respiratory complex I.
Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov L
Nature (2022)
PMID: 36104567
Related structures: EMD-14648

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-105804 (preferred)
Entry contents:
44 distinct polypeptide molecules
Macromolecules (44 distinct):
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:
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chain: V
Molecule details ›
Chain: V
Length: 140 amino acids
Theoretical weight: 14.65 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A8N7XJ91 (Residues: 2-141; Coverage: 99%)
Gene name: JEQ12_016431
Sequence domains: Tim17/Tim22/Tim23/Pmp24 family
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial Chain: W
Molecule details ›
Chain: W
Length: 139 amino acids
Theoretical weight: 16.32 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A8N7XJ68 (Residues: 51-189; Coverage: 74%)
Gene name: JEQ12_001574
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit
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: 171 amino acids
Theoretical weight: 20.01 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A8N7XJG2 (Residues: 2-172; Coverage: 99%)
Gene name: JEQ12_013613
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 Chain: Z
Molecule details ›
Chain: Z
Length: 171 amino acids
Theoretical weight: 20.53 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P3EI17 (Residues: 4-174; Coverage: 97%)
Gene name: JEQ12_012218
Sequence domains: NADH-ubiquinone oxidoreductase subunit 10
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chain: k
Molecule details ›
Chain: k
Length: 320 amino acids
Theoretical weight: 36.88 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A8N7XJK5 (Residues: 36-355; Coverage: 90%)
Gene name: JEQ12_000054
Sequence domains: Deoxynucleoside kinase
Complex I-15 kDa Chain: l
Molecule details ›
Chain: l
Length: 105 amino acids
Theoretical weight: 12.47 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A836D7R1 (Residues: 192-296; Coverage: 36%)
Gene name: JEQ12_000171
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 Chain: m
Molecule details ›
Chain: m
Length: 80 amino acids
Theoretical weight: 8.87 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A836A4Q3 (Residues: 42-121; Coverage: 66%)
Gene name: JEQ12_005750
Sequence domains: NADH dehydrogenase 1 alpha subcomplex subunit 3
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 Chain: n
Molecule details ›
Chain: n
Length: 79 amino acids
Theoretical weight: 8.96 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P7DQB1 (Residues: 12-90; Coverage: 81%)
Gene name: JEQ12_009750
Sequence domains: NADH-ubiquinone oxidoreductase B12 subunit family
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chain: o
Molecule details ›
Chain: o
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: p
Molecule details ›
Chain: p
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: q
Molecule details ›
Chain: q
Length: 139 amino acids
Theoretical weight: 16.28 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P3E975 (Residues: 6-144; Coverage: 97%)
Sequence domains: GRIM-19 protein
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 dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: s
Molecule details ›
Chain: s
Length: 122 amino acids
Theoretical weight: 14.96 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A8N7XJH2 (Residues: 2-123; Coverage: 89%)
Gene name: JEQ12_016212
Sequence domains: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: t
Molecule details ›
Chain: t
Length: 177 amino acids
Theoretical weight: 21.52 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P3E749 (Residues: 2-178; Coverage: 99%)
Gene name: JEQ12_019240
Sequence domains: Complex 1 protein (LYR family)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial Chain: u
Molecule details ›
Chain: u
Length: 65 amino acids
Theoretical weight: 7.9 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A8N7XJB4 (Residues: 41-105; Coverage: 60%)
Gene name: JEQ12_015775
Sequence domains: NADH dehydrogenase 1 beta subcomplex subunit 2
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: v
Molecule details ›
Chain: v
Length: 155 amino acids
Theoretical weight: 18.52 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5Q1B0 (Residues: 32-186; Coverage: 83%)
Gene name: NDUFB8
Sequence domains: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial Chain: w
Molecule details ›
Chain: w
Length: 101 amino acids
Theoretical weight: 12 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A836CQA7 (Residues: 48-148; Coverage: 67%)
Gene name: JEQ12_020035
Sequence domains: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I)
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial Chain: x
Molecule details ›
Chain: x
Length: 49 amino acids
Theoretical weight: 5.81 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P3EDV0 (Residues: 28-76; Coverage: 65%)
Sequence domains: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 Chain: y
Molecule details ›
Chain: y
Length: 50 amino acids
Theoretical weight: 6.15 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A7M4DUG1 (Residues: 9-58; Coverage: 86%)
Sequence domains: MNLL subunit
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: z
Molecule details ›
Chain: z
Length: 70 amino acids
Theoretical weight: 8.21 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P9FRJ5 (Residues: 1-70; Coverage: 100%)
Sequence domains: NADH-ubiquinone oxidoreductase MWFE subunit
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: 1
Molecule details ›
Chain: 1
Length: 430 amino acids
Theoretical weight: 47.19 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PUX0 (Residues: 29-458; Coverage: 93%)
Gene name: NDUFV1
Sequence domains:
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: 2
Molecule details ›
Chain: 2
Length: 213 amino acids
Theoretical weight: 23.6 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5NRY1 (Residues: 34-246; Coverage: 87%)
Gene name: NDUFV2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial Chain: 3
Molecule details ›
Chain: 3
Length: 688 amino acids
Theoretical weight: 75.52 KDa
Source organism: Ovis aries
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chain: 4
Molecule details ›
Chain: 4
Length: 430 amino acids
Theoretical weight: 49.22 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P3DZ89 (Residues: 34-463; Coverage: 93%)
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial Chain: 5
Molecule details ›
Chain: 5
Length: 208 amino acids
Theoretical weight: 24.38 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PB27 (Residues: 45-252; Coverage: 78%)
Gene name: NDUFS3
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chain: 6
Molecule details ›
Chain: 6
Length: 156 amino acids
Theoretical weight: 17.86 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P7E5N1 (Residues: 68-223; Coverage: 70%)
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial Chain: 9
Molecule details ›
Chain: 9
Length: 217 amino acids
Theoretical weight: 24.5 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P3TFB2 (Residues: 1-217; Coverage: 100%)
Sequence domains: 4Fe-4S dicluster domain
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial Chain: a
Molecule details ›
Chain: a
Length: 44 amino acids
Theoretical weight: 5.26 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P3E7B5 (Residues: 66-109; Coverage: 40%)
Sequence domains: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: b
Molecule details ›
Chain: b
Length: 95 amino acids
Theoretical weight: 10.51 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P7EX23 (Residues: 29-123; Coverage: 77%)
Gene name: JEQ12_007015
Sequence domains: Zinc-finger domain
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 126 amino acids
Theoretical weight: 14.56 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5PE07 (Residues: 45-170; Coverage: 74%)
Gene name: NDUFS4
Sequence domains: NADH dehydrogenase ubiquinone Fe-S protein 4
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chain: d
Molecule details ›
Chain: d
Length: 340 amino acids
Theoretical weight: 38.86 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A6P3E3I5 (Residues: 36-375; Coverage: 90%)
Gene name: JEQ12_015054
Sequence domains: NAD dependent epimerase/dehydratase family
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: e
Molecule details ›
Chain: e
Length: 86 amino acids
Theoretical weight: 9.84 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A8N7XJ49 (Residues: 14-99; Coverage: 87%)
Gene name: JEQ12_016867
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chain: f
Molecule details ›
Chain: f
Length: 113 amino acids
Theoretical weight: 13.03 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: A0A836ABR5 (Residues: 4-116; Coverage: 97%)
Gene name: JEQ12_009905
Sequence domains: ETC complex I subunit conserved region
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: g
Molecule details ›
Chain: g
Length: 114 amino acids
Theoretical weight: 13.77 KDa
Source organism: Ovis aries
UniProt:
  • Canonical: W5QC06 (Residues: 27-140; Coverage: 81%)
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
UniProt:
  • Canonical: A0A8N7XJ18 (Residues: 1-145; Coverage: 100%)
Gene name: JEQ12_014294
Sequence domains: NADH ubiquinone oxidoreductase subunit NDUFA12

Ligands and Environments

12 bound ligands:
Ligand 3PE 13 x 3PE
Ligand PC1 5 x PC1
Ligand ZMP 2 x ZMP
Ligand AMP 1 x AMP
Ligand MYR 1 x MYR
Ligand SF4 6 x SF4
Ligand FMN 1 x FMN
Ligand NAI 1 x NAI
Ligand FES 2 x FES
Ligand K 1 x K
Ligand ZN 1 x ZN
Ligand NDP 1 x NDP
4 modified residues:
Ligand FME 3 x FME
Ligand AYA 2 x AYA
Ligand SEP 1 x SEP
Ligand 2MR 1 x 2MR

Experiments and Validation Details

Entry percentile scores
Resolution: 3.46Å
Relevant EMDB volumes: EMD-14648

Quick links

Citations

4 review citations

The functional significance of mitochondrial respiratory chain supercomplexes.
Kohler et al. (2023)
3 more