› 5ldx

Electron Microscopy
5.6Å resolution

Structure of mammalian respiratory Complex I, class3.

Released:
DOI: 10.2210/pdb5ldx/pdb
PDB entry 5ldx coloured by chain, front view.
PDB entry 5ldx coloured by chain, side view.
PDB entry 5ldx coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Structure of mammalian respiratory complex I.
Zhu J, Vinothkumar KR, Hirst J
Nature 536 354-358 (2016)
PMID: 27509854
Related structures: EMD-4041

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-132196 (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: 13.06 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03898 (Residues: 1-115; Coverage: 100%)
Gene names: MT-ND3, MTND3, NADH3, ND3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 179 amino acids
Theoretical weight: 20.1 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P42026 (Residues: 38-216; Coverage: 83%)
Gene name: NDUFS7
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial Chain: C
Molecule details ›
Chain: C
Length: 228 amino acids
Theoretical weight: 26.46 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P23709 (Residues: 39-266; Coverage: 86%)
Gene name: NDUFS3
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 429 amino acids
Theoretical weight: 49.17 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P17694 (Residues: 35-463; Coverage: 93%)
Gene name: NDUFS2
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: E
Molecule details ›
Chain: E
Length: 217 amino acids
Theoretical weight: 23.84 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P04394 (Residues: 33-249; Coverage: 87%)
Gene name: NDUFV2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: F
Molecule details ›
Chain: F
Length: 444 amino acids
Theoretical weight: 48.56 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P25708 (Residues: 21-464; Coverage: 96%)
Gene names: NDUFV1, UQOR1
Sequence domains:
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial Chain: G
Molecule details ›
Chain: G
Length: 700 amino acids
Theoretical weight: 64.61 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P15690 (Residues: 31-232; Coverage: 28%)
Gene name: NDUFS1
Sequence domains:
NADH-ubiquinone oxidoreductase chain 1 Chain: H
Molecule details ›
Chain: H
Length: 318 amino acids
Theoretical weight: 35.69 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03887 (Residues: 1-318; Coverage: 100%)
Gene names: MT-ND1, MTND1, NADH1, ND1
Sequence domains: NADH dehydrogenase
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial Chain: I
Molecule details ›
Chain: I
Length: 176 amino acids
Theoretical weight: 20.22 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P42028 (Residues: 37-212; Coverage: 83%)
Gene name: NDUFS8
Sequence domains: 4Fe-4S dicluster domain
NADH-ubiquinone oxidoreductase chain 6 Chain: J
Molecule details ›
Chain: J
Length: 175 amino acids
Theoretical weight: 19.08 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03924 (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: 10.8 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03902 (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: 68.33 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03920 (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: 52.13 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03910 (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: 39.27 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03892 (Residues: 1-347; Coverage: 100%)
Gene names: MT-ND2, MTND2, NADH2, ND2
Sequence domains:
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chain: O
Molecule details ›
Chain: O
Length: 314 amino acids
Theoretical weight: 34.01 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P34942 (Residues: 114-341; Coverage: 67%)
Gene name: NDUFA10
Sequence domains: Deoxynucleoside kinase
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, NDUFA9 Chain: P
Molecule details ›
Chain: P
Length: 283 amino acids
Theoretical weight: 24.1 KDa
Source organism: Bos taurus
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, NDUFS4 Chain: Q
Molecule details ›
Chain: Q
Length: 113 amino acids
Theoretical weight: 9.63 KDa
Source organism: Bos taurus
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: R
Molecule details ›
Chain: R
Length: 89 amino acids
Theoretical weight: 8.32 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P23934 (Residues: 87-121; Coverage: 28%)
Gene name: NDUFS6
Sequence domains: Zinc-finger domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: S
Molecule details ›
Chain: S
Length: 99 amino acids
Theoretical weight: 11.1 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02370 (Residues: 1-99; Coverage: 100%)
Gene name: NDUFA2
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Acyl carrier protein, mitochondrial Chains: T, U
Molecule details ›
Chains: T, U
Length: 88 amino acids
Theoretical weight: 10.12 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P52505 (Residues: 69-156; Coverage: 56%)
Gene name: NDUFAB1
Sequence domains: Phosphopantetheine attachment site
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chain: V
Molecule details ›
Chain: V
Length: 115 amino acids
Theoretical weight: 13.2 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P23935 (Residues: 2-116; Coverage: 99%)
Gene name: NDUFA5
Sequence domains: ETC complex I subunit conserved region
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: W
Molecule details ›
Chain: W
Length: 127 amino acids
Theoretical weight: 14.95 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02366 (Residues: 2-128; Coverage: 99%)
Gene name: NDUFA6
Sequence domains: Complex1_LYR-like
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: X
Molecule details ›
Chain: X
Length: 164 amino acids
Theoretical weight: 17.62 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P42029 (Residues: 6-114; Coverage: 63%)
Gene name: NDUFA8
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chain: Y
Molecule details ›
Chain: Y
Length: 140 amino acids
Theoretical weight: 14.64 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q8HXG6 (Residues: 2-141; Coverage: 99%)
Gene name: NDUFA11
Sequence domains: Tim17/Tim22/Tim23/Pmp24 family
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: Z
Molecule details ›
Chain: Z
Length: 138 amino acids
Theoretical weight: 14.14 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q95KV7 (Residues: 32-100; Coverage: 48%)
Gene names: GRIM19, NDUFA13
Sequence domains: GRIM-19 protein
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: a
Molecule details ›
Chain: a
Length: 70 amino acids
Theoretical weight: 8.12 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02377 (Residues: 1-70; Coverage: 100%)
Gene name: NDUFA1
Sequence domains: NADH-ubiquinone oxidoreductase MWFE subunit
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 Chain: b
Molecule details ›
Chain: b
Length: 80 amino acids
Theoretical weight: 7.86 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02371 (Residues: 2-46; Coverage: 54%)
Gene name: NDUFA3
Sequence domains: NADH dehydrogenase 1 alpha subcomplex subunit 3
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 49 amino acids
Theoretical weight: 5.84 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02376 (Residues: 28-76; Coverage: 65%)
Gene name: NDUFC1
Sequence domains: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chain: d
Molecule details ›
Chain: d
Length: 114 amino acids
Theoretical weight: 11.99 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02827 (Residues: 29-97; Coverage: 58%)
Gene name: NDUFC2
Sequence domains: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2)
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 Chain: e
Molecule details ›
Chain: e
Length: 106 amino acids
Theoretical weight: 12.69 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02379 (Residues: 1-106; Coverage: 100%)
Gene name: NDUFS5
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 Chain: f
Molecule details ›
Chain: f
Length: 57 amino acids
Theoretical weight: 6.98 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02378 (Residues: 1-57; Coverage: 100%)
Gene name: NDUFB1
Sequence domains: MNLL subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial Chain: g
Molecule details ›
Chain: g
Length: 125 amino acids
Theoretical weight: 14.47 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q8HXG5 (Residues: 30-154; Coverage: 81%)
Gene name: NDUFB11
Sequence domains: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial Chain: h
Molecule details ›
Chain: h
Length: 134 amino acids
Theoretical weight: 12.61 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02380 (Residues: 53-91; Coverage: 21%)
Gene name: NDUFB5
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 Chain: i
Molecule details ›
Chain: i
Length: 106 amino acids
Theoretical weight: 10.23 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02367 (Residues: 7-33; Coverage: 21%)
Gene name: NDUFB6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2 Chain: j
Molecule details ›
Chain: j
Length: 52 amino acids
Theoretical weight: 4.44 KDa
Source organism: Bos taurus
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3 Chain: k
Molecule details ›
Chain: k
Length: 74 amino acids
Theoretical weight: 6.32 KDa
Source organism: Bos taurus
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8 Chain: l
Molecule details ›
Chain: l
Length: 118 amino acids
Theoretical weight: 10.06 KDa
Source organism: Bos taurus
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Chain: m
Molecule details ›
Chain: m
Length: 118 amino acids
Theoretical weight: 13.42 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P48305 (Residues: 33-129; Coverage: 75%)
Gene name: NDUFB4
Sequence domains: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: n
Molecule details ›
Chain: n
Length: 166 amino acids
Theoretical weight: 19.25 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02369 (Residues: 11-137; Coverage: 71%)
Gene names: NDUFB9, UQOR22
Sequence domains: Complex 1 protein (LYR family)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: o
Molecule details ›
Chain: o
Length: 58 amino acids
Theoretical weight: 7.58 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02368 (Residues: 58-115; Coverage: 42%)
Gene name: NDUFB7
Sequence domains: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 Chain: p
Molecule details ›
Chain: p
Length: 169 amino acids
Theoretical weight: 16.91 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02373 (Residues: 77-143; Coverage: 38%)
Gene name: NDUFB10
Sequence domains: NADH-ubiquinone oxidoreductase subunit 10
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Chain: q
Molecule details ›
Chain: q
Length: 138 amino acids
Theoretical weight: 16.31 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: O97725 (Residues: 2-139; Coverage: 95%)
Gene name: NDUFA12
Sequence domains: NADH ubiquinone oxidoreductase subunit NDUFA12
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7 Chain: r
Molecule details ›
Chain: r
Length: 87 amino acids
Theoretical weight: 7.42 KDa
Source organism: Bos taurus
NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3 Chain: s
Molecule details ›
Chain: s
Length: 35 amino acids
Theoretical weight: 3 KDa
Source organism: Bos taurus

Ligands and Environments

5 bound ligands:
Ligand SF4 6 x SF4
Ligand FES 2 x FES
Ligand FMN 1 x FMN
Ligand NAP 1 x NAP
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.6Å
Relevant EMDB volumes: EMD-4041

Quick links

Citations

65 review citations

Iron-sulfur cluster biogenesis and trafficking in mitochondria.
Braymer et al. (2017)
64 more

8 mentions without citation

Structure of mammalian respiratory complex I.
Zhu et al. (2016)
7 more