› 5lc5

Electron Microscopy
4.35Å resolution

Structure of mammalian respiratory Complex I, class2

Released:
DOI: 10.2210/pdb5lc5/pdb
PDB entry 5lc5 coloured by chain, front view.
PDB entry 5lc5 coloured by chain, side view.
PDB entry 5lc5 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-4032

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-132194 (preferred)
Entry contents:
45 distinct polypeptide molecules
Macromolecules (45 distinct):
NADH-ubiquinone oxidoreductase chain 3 Chain: A
Molecule details ›
Chain: A
Length: 111 amino acids
Theoretical weight: 12.51 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03898 (Residues: 2-112; Coverage: 97%)
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: 147 amino acids
Theoretical weight: 16.63 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P42026 (Residues: 64-210; Coverage: 68%)
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: 206 amino acids
Theoretical weight: 24.2 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P23709 (Residues: 46-251; Coverage: 77%)
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: 426 amino acids
Theoretical weight: 48.69 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P17694 (Residues: 38-463; Coverage: 92%)
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: 249 amino acids
Theoretical weight: 27.34 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P04394 (Residues: 1-249; Coverage: 100%)
Gene name: NDUFV2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: F
Molecule details ›
Chain: F
Length: 464 amino acids
Theoretical weight: 50.72 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P25708 (Residues: 1-464; Coverage: 100%)
Gene names: NDUFV1, UQOR1
Sequence domains:
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial Chain: G
Molecule details ›
Chain: G
Length: 715 amino acids
Theoretical weight: 66.44 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P15690 (Residues: 1-232; Coverage: 32%)
Gene name: NDUFS1
Sequence domains:
NADH-ubiquinone oxidoreductase chain 1 Chain: H
Molecule details ›
Chain: H
Length: 313 amino acids
Theoretical weight: 35.08 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03887 (Residues: 3-315; Coverage: 98%)
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: 171 amino acids
Theoretical weight: 18.62 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03924 (Residues: 2-172; Coverage: 98%)
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: 95 amino acids
Theoretical weight: 10.44 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03902 (Residues: 2-96; Coverage: 97%)
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: 604 amino acids
Theoretical weight: 68.07 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03920 (Residues: 2-605; Coverage: 100%)
Gene names: MT-ND5, MTND5, NADH5, ND5
Sequence domains:
NADH-ubiquinone oxidoreductase chain 4 Chain: M
Molecule details ›
Chain: M
Length: 457 amino acids
Theoretical weight: 51.89 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03910 (Residues: 3-459; Coverage: 100%)
Gene names: MT-ND4, MTND4, NADH4, ND4
Sequence domains:
NADH-ubiquinone oxidoreductase chain 2 Chain: N
Molecule details ›
Chain: N
Length: 344 amino acids
Theoretical weight: 38.9 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P03892 (Residues: 2-345; Coverage: 99%)
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, mitochondrial Chain: P
Molecule details ›
Chain: P
Length: 335 amino acids
Theoretical weight: 28.53 KDa
Source organism: Bos taurus
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial 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: 80 amino acids
Theoretical weight: 9.27 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02370 (Residues: 17-96; Coverage: 81%)
Gene name: NDUFA2
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Acyl carrier protein, mitochondrial Chain: T
Molecule details ›
Chain: T
Length: 75 amino acids
Theoretical weight: 8.67 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P52505 (Residues: 76-150; Coverage: 48%)
Gene name: NDUFAB1
Sequence domains: Phosphopantetheine attachment site
Acyl carrier protein, mitochondrial Chain: U
Molecule details ›
Chain: U
Length: 85 amino acids
Theoretical weight: 9.85 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P52505 (Residues: 72-156; Coverage: 55%)
Gene name: NDUFAB1
Sequence domains: Phosphopantetheine attachment site
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chain: V
Molecule details ›
Chain: V
Length: 116 amino acids
Theoretical weight: 13.33 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P23935 (Residues: 1-116; Coverage: 100%)
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: 128 amino acids
Theoretical weight: 15.08 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02366 (Residues: 1-128; Coverage: 100%)
Gene name: NDUFA6
Sequence domains: Complex1_LYR-like
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: X
Molecule details ›
Chain: X
Length: 169 amino acids
Theoretical weight: 18.12 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P42029 (Residues: 1-114; Coverage: 66%)
Gene name: NDUFA8
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chain: Y
Molecule details ›
Chain: Y
Length: 138 amino acids
Theoretical weight: 14.41 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q8HXG6 (Residues: 2-139; Coverage: 98%)
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: 76 amino acids
Theoretical weight: 8.8 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02376 (Residues: 1-76; Coverage: 100%)
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: 154 amino acids
Theoretical weight: 17.59 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q8HXG5 (Residues: 1-154; Coverage: 100%)
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: 186 amino acids
Theoretical weight: 18.07 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02380 (Residues: 1-91; Coverage: 48%)
Gene name: NDUFB5
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 Chain: i
Molecule details ›
Chain: i
Length: 121 amino acids
Theoretical weight: 11.64 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02367 (Residues: 1-33; Coverage: 26%)
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: 4.35Å
Relevant EMDB volumes: EMD-4032

Quick links

Citations

62 review citations

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

25 mentions without citation

Mitochondrial Structure and Bioenergetics in Normal and Disease Conditions.
Protasoni et al. (2021)
24 more