› 8q0q

Electron Microscopy
3.6Å resolution

Outward-facing, slack proteoliposome complex I at 3.6 A. Initially purified in DDM

Released:
DOI: 10.2210/pdb8q0q/pdb
PDB entry 8q0q coloured by chain, front view.
PDB entry 8q0q coloured by chain, side view.
PDB entry 8q0q coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I.
Grba DN, Wright JJ, Yin Z, Fisher W, Hirst J
Science 384 1247-1253 (2024)
PMID: 38870289
Related structures: EMD-18059

Function and Biology Details

Reaction catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 45-mer (preferred)
PDBe Complex ID:
PDB-CPX-245042 (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: 13.09 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q7JAS9 (Residues: 1-115; Coverage: 100%)
Gene names: ND3, nad3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 216 amino acids
Theoretical weight: 23.8 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P42026 (Residues: 1-216; Coverage: 100%)
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: 266 amino acids
Theoretical weight: 30.32 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P23709 (Residues: 1-266; Coverage: 100%)
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: 463 amino acids
Theoretical weight: 52.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P17694 (Residues: 1-463; Coverage: 100%)
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: 727 amino acids
Theoretical weight: 79.53 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P15690 (Residues: 1-727; Coverage: 100%)
Gene name: NDUFS1
Sequence domains:
NADH-ubiquinone oxidoreductase chain 1 Chain: H
Molecule details ›
Chain: H
Length: 318 amino acids
Theoretical weight: 35.72 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: 212 amino acids
Theoretical weight: 23.93 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P42028 (Residues: 1-212; Coverage: 100%)
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: 19.11 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: 10.83 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: 68.36 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: 52.16 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: 39.3 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: 343 amino acids
Theoretical weight: 39.33 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P34942 (Residues: 1-343; Coverage: 100%)
Gene name: NDUFA10
Sequence domains: Deoxynucleoside kinase
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chain: P
Molecule details ›
Chain: P
Length: 380 amino acids
Theoretical weight: 42.91 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P34943 (Residues: 1-380; Coverage: 100%)
Gene name: NDUFA9
Sequence domains: NAD dependent epimerase/dehydratase family
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 175 amino acids
Theoretical weight: 19.84 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02375 (Residues: 1-175; Coverage: 100%)
Gene name: NDUFS4
Sequence domains: NADH dehydrogenase ubiquinone Fe-S protein 4
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: R
Molecule details ›
Chain: R
Length: 124 amino acids
Theoretical weight: 13.43 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P23934 (Residues: 1-124; Coverage: 100%)
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: 156 amino acids
Theoretical weight: 17.42 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P52505 (Residues: 1-156; Coverage: 100%)
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: 172 amino acids
Theoretical weight: 20.12 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P42029 (Residues: 1-172; Coverage: 100%)
Gene name: NDUFA8
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chain: Y
Molecule details ›
Chain: Y
Length: 141 amino acids
Theoretical weight: 14.77 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q8HXG6 (Residues: 1-141; Coverage: 100%)
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: 144 amino acids
Theoretical weight: 16.69 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q95KV7 (Residues: 1-144; Coverage: 100%)
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: 84 amino acids
Theoretical weight: 9.4 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02371 (Residues: 1-84; Coverage: 100%)
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: 120 amino acids
Theoretical weight: 14.16 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02827 (Residues: 1-120; Coverage: 100%)
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: 189 amino acids
Theoretical weight: 21.62 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02380 (Residues: 1-189; Coverage: 100%)
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: 128 amino acids
Theoretical weight: 15.59 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02367 (Residues: 1-128; Coverage: 100%)
Gene name: NDUFB6
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial Chain: j
Molecule details ›
Chain: j
Length: 108 amino acids
Theoretical weight: 12.3 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02374 (Residues: 1-108; Coverage: 100%)
Gene name: NDUFB2
Sequence domains: NADH dehydrogenase 1 beta subcomplex subunit 2
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 Chain: k
Molecule details ›
Chain: k
Length: 98 amino acids
Theoretical weight: 11.16 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02365 (Residues: 1-98; Coverage: 100%)
Gene name: NDUFB3
Sequence domains: NADH-ubiquinone oxidoreductase B12 subunit family
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: l
Molecule details ›
Chain: l
Length: 186 amino acids
Theoretical weight: 21.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02372 (Residues: 1-186; Coverage: 100%)
Gene name: NDUFB8
Sequence domains: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Chain: m
Molecule details ›
Chain: m
Length: 129 amino acids
Theoretical weight: 15.25 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P48305 (Residues: 1-129; Coverage: 100%)
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: 179 amino acids
Theoretical weight: 21.83 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02369 (Residues: 1-179; Coverage: 100%)
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: 137 amino acids
Theoretical weight: 16.43 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02368 (Residues: 1-137; Coverage: 100%)
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: 176 amino acids
Theoretical weight: 21 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q02373 (Residues: 1-176; Coverage: 100%)
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: 145 amino acids
Theoretical weight: 17.16 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: O97725 (Residues: 1-145; Coverage: 100%)
Gene name: NDUFA12
Sequence domains: NADH ubiquinone oxidoreductase subunit NDUFA12
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 Chain: r
Molecule details ›
Chain: r
Length: 113 amino acids
Theoretical weight: 12.74 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q05752 (Residues: 1-113; Coverage: 100%)
Gene names: CI-B14-5A, NDUFA7
Sequence domains: NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a)
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial Chain: s
Molecule details ›
Chain: s
Length: 109 amino acids
Theoretical weight: 11.87 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P25712 (Residues: 1-109; Coverage: 100%)
Gene name: NDUFV3
Sequence domains: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

Ligands and Environments

14 bound ligands:
Ligand 3PE 10 x 3PE
Ligand PC1 5 x PC1
Ligand SF4 6 x SF4
Ligand FES 2 x FES
Ligand FMN 1 x FMN
Ligand K 1 x K
Ligand CDL 4 x CDL
Ligand DGT 1 x DGT
Ligand MG 1 x MG
Ligand NDP 1 x NDP
Ligand ZN 1 x ZN
Ligand EHZ 2 x EHZ
Ligand CHD 1 x CHD
Ligand MYR 1 x MYR
4 modified residues:
Ligand FME 7 x FME
Ligand 2MR 1 x 2MR
Ligand AYA 2 x AYA
Ligand SAC 2 x SAC

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-18059

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