› 8uex

Electron Microscopy
3.9Å resolution

In-situ complex I, Deactive class06

Released:
DOI: 10.2210/pdb8uex/pdb
PDB entry 8uex coloured by chain, front view.
PDB entry 8uex coloured by chain, side view.
PDB entry 8uex coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
High-resolution in situ structures of mammalian respiratory supercomplexes.
Zheng W, Chai P, Zhu J, Zhang K
Nature (2024)
PMID: 38811722
Related structures: EMD-42174

Function and Biology Details

Reaction catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 45-mer (preferred)
PDBe Complex ID:
PDB-CPX-245926 (preferred)
Entry contents:
44 distinct polypeptide molecules
Macromolecules (44 distinct):
NADH-ubiquinone oxidoreductase chain 3 Chain: 1A
Molecule details ›
Chain: 1A
Length: 115 amino acids
Theoretical weight: 13.03 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79880 (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: 1B
Molecule details ›
Chain: 1B
Length: 258 amino acids
Theoretical weight: 28.5 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VVS8 (Residues: 1-258; Coverage: 100%)
Gene name: NDUFS7
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial Chain: 1C
Molecule details ›
Chain: 1C
Length: 264 amino acids
Theoretical weight: 30.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZNN4 (Residues: 1-264; Coverage: 100%)
Gene name: NDUFS3
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chain: 1D
Molecule details ›
Chain: 1D
Length: 476 amino acids
Theoretical weight: 54.17 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0QM68 (Residues: 1-476; Coverage: 100%)
Gene name: NDUFS2
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: 1E
Molecule details ›
Chain: 1E
Length: 249 amino acids
Theoretical weight: 27.44 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VRV3 (Residues: 1-249; Coverage: 100%)
Gene name: NDUFV2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: 1F
Molecule details ›
Chain: 1F
Length: 464 amino acids
Theoretical weight: 50.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1SZP7 (Residues: 1-464; Coverage: 100%)
Gene name: NDUFV1
Sequence domains:
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial Chain: 1G
Molecule details ›
Chain: 1G
Length: 727 amino acids
Theoretical weight: 79.63 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ARY3 (Residues: 14-740; Coverage: 98%)
Gene name: NDUFS1
Sequence domains:
NADH-ubiquinone oxidoreductase chain 1 Chain: 1H
Molecule details ›
Chain: 1H
Length: 318 amino acids
Theoretical weight: 35.62 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0U1RS44 (Residues: 1-318; Coverage: 100%)
Gene names: MT-ND1, ND1
Sequence domains: NADH dehydrogenase
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial Chain: 1I
Molecule details ›
Chain: 1I
Length: 239 amino acids
Theoretical weight: 27.14 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZUN9 (Residues: 1-239; Coverage: 100%)
Gene name: NDUFS8
Sequence domains: 4Fe-4S dicluster domain
NADH-ubiquinone oxidoreductase chain 6 Chain: 1J
Molecule details ›
Chain: 1J
Length: 175 amino acids
Theoretical weight: 19.05 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79882 (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: 1K
Molecule details ›
Chain: 1K
Length: 98 amino acids
Theoretical weight: 10.86 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P56632 (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: 1L
Molecule details ›
Chain: 1L
Length: 606 amino acids
Theoretical weight: 68.72 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q9TDR1 (Residues: 1-606; Coverage: 100%)
Gene names: MT-ND5, MTND5, NADH5, ND5
Sequence domains:
NADH-ubiquinone oxidoreductase chain 4 Chain: 1M
Molecule details ›
Chain: 1M
Length: 459 amino acids
Theoretical weight: 51.89 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79881 (Residues: 1-459; Coverage: 100%)
Gene names: MT-ND4, MTND4, NADH4, ND4
Sequence domains:
NADH-ubiquinone oxidoreductase chain 2 Chain: 1N
Molecule details ›
Chain: 1N
Length: 347 amino acids
Theoretical weight: 39.11 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79875 (Residues: 1-347; Coverage: 100%)
Gene names: MT-ND2, MTND2, NADH2, ND2
Sequence domains:
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chain: 1O
Molecule details ›
Chain: 1O
Length: 357 amino acids
Theoretical weight: 40.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SIS9 (Residues: 1-357; Coverage: 100%)
Gene name: NDUFA10
Sequence domains: Deoxynucleoside kinase
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chain: 1P
Molecule details ›
Chain: 1P
Length: 377 amino acids
Theoretical weight: 42.61 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1ULW2 (Residues: 1-377; Coverage: 100%)
Gene name: NDUFA9
Sequence domains: NAD dependent epimerase/dehydratase family
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: 1Q
Molecule details ›
Chain: 1Q
Length: 175 amino acids
Theoretical weight: 19.75 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1SN37 (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: 1R
Molecule details ›
Chain: 1R
Length: 123 amino acids
Theoretical weight: 13.35 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1THU2 (Residues: 1-123; Coverage: 100%)
Gene name: NDUFS6
Sequence domains: Zinc-finger domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: 1S
Molecule details ›
Chain: 1S
Length: 99 amino acids
Theoretical weight: 11.1 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1FN21 (Residues: 1-99; Coverage: 100%)
Gene name: NDUFA2
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Acyl carrier protein Chains: 1T, 1U
Molecule details ›
Chains: 1T, 1U
Length: 156 amino acids
Theoretical weight: 17.34 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1KH26 (Residues: 1-156; Coverage: 100%)
Gene name: NDUFAB1
Sequence domains: Phosphopantetheine attachment site
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chain: 1V
Molecule details ›
Chain: 1V
Length: 116 amino acids
Theoretical weight: 13.32 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0UWW0 (Residues: 1-116; Coverage: 99%)
Sequence domains: ETC complex I subunit conserved region
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: 1W
Molecule details ›
Chain: 1W
Length: 128 amino acids
Theoretical weight: 14.95 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A480VKQ8 (Residues: 1-128; Coverage: 100%)
Sequence domains: Complex 1 protein (LYR family)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: 1X
Molecule details ›
Chain: 1X
Length: 172 amino acids
Theoretical weight: 20.06 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0K6B5 (Residues: 77-248; Coverage: 69%)
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chain: 1Y
Molecule details ›
Chain: 1Y
Length: 141 amino acids
Theoretical weight: 14.69 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGM4 (Residues: 1-141; Coverage: 100%)
Gene name: NDUFA11
Sequence domains: Tim17/Tim22/Tim23/Pmp24 family
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: 1Z
Molecule details ›
Chain: 1Z
Length: 144 amino acids
Theoretical weight: 16.91 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0K655 (Residues: 1-144; Coverage: 100%)
Gene name: NDUFA13
Sequence domains: GRIM-19 protein
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: 1a
Molecule details ›
Chain: 1a
Length: 70 amino acids
Theoretical weight: 8.03 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0TJQ4 (Residues: 92-161; Coverage: 44%)
Sequence domains: NADH-ubiquinone oxidoreductase MWFE subunit
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 Chain: 1b
Molecule details ›
Chain: 1b
Length: 84 amino acids
Theoretical weight: 9.23 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VQ42 (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: 1c
Molecule details ›
Chain: 1c
Length: 76 amino acids
Theoretical weight: 8.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1EYQ2 (Residues: 77-152; Coverage: 50%)
Sequence domains: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chain: 1d
Molecule details ›
Chain: 1d
Length: 123 amino acids
Theoretical weight: 14.35 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A480JRW3 (Residues: 1-122; Coverage: 100%)
Gene name: NDUFC2
Sequence domains: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2)
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 Chain: 1e
Molecule details ›
Chain: 1e
Length: 106 amino acids
Theoretical weight: 12.51 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VX77 (Residues: 1-106; Coverage: 100%)
Gene name: NDUFS5
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 Chain: 1f
Molecule details ›
Chain: 1f
Length: 135 amino acids
Theoretical weight: 15.37 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1IZ33 (Residues: 1-106; Coverage: 100%)
Sequence domains: MNLL subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial Chain: 1g
Molecule details ›
Chain: 1g
Length: 154 amino acids
Theoretical weight: 17.38 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1EYI7 (Residues: 1-154; Coverage: 100%)
Sequence domains: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial Chain: 1h
Molecule details ›
Chain: 1h
Length: 189 amino acids
Theoretical weight: 21.59 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SGC6 (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: 1i
Molecule details ›
Chain: 1i
Length: 128 amino acids
Theoretical weight: 15.65 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1UIV8 (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: 1j
Molecule details ›
Chain: 1j
Length: 105 amino acids
Theoretical weight: 11.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1G9F4 (Residues: 1-105; Coverage: 100%)
Gene name: NDUFB2
Sequence domains: NADH dehydrogenase 1 beta subcomplex subunit 2
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 Chain: 1k
Molecule details ›
Chain: 1k
Length: 98 amino acids
Theoretical weight: 11.13 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VD84 (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: 1l
Molecule details ›
Chain: 1l
Length: 186 amino acids
Theoretical weight: 21.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: B8Y651 (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: 1m
Molecule details ›
Chain: 1m
Length: 129 amino acids
Theoretical weight: 15.12 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1T6M0 (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: 1n
Molecule details ›
Chain: 1n
Length: 179 amino acids
Theoretical weight: 21.86 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GSE5 (Residues: 43-221; Coverage: 81%)
Gene name: NDUFB9
Sequence domains: Complex 1 protein (LYR family)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: 1o
Molecule details ›
Chain: 1o
Length: 137 amino acids
Theoretical weight: 16.49 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SCH1 (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: 1p
Molecule details ›
Chain: 1p
Length: 176 amino acids
Theoretical weight: 20.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0R7A9 (Residues: 124-299; Coverage: 59%)
Sequence domains: NADH-ubiquinone oxidoreductase subunit 10
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Chain: 1q
Molecule details ›
Chain: 1q
Length: 145 amino acids
Theoretical weight: 17.16 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SQP4 (Residues: 1-145; Coverage: 100%)
Gene name: NDUFA12
Sequence domains: NADH ubiquinone oxidoreductase subunit NDUFA12
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 Chain: 1r
Molecule details ›
Chain: 1r
Length: 114 amino acids
Theoretical weight: 12.67 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8W4F7N8 (Residues: 2-113; Coverage: 99%)
Gene name: NDUFA7
Sequence domains: NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a)
NADH:ubiquinone oxidoreductase subunit V3 Chain: 1s
Molecule details ›
Chain: 1s
Length: 471 amino acids
Theoretical weight: 48.22 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TE42 (Residues: 1-471; Coverage: 100%)
Gene name: NDUFV3
Sequence domains: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

Ligands and Environments

14 bound ligands:
Ligand 3PE 6 x 3PE
Ligand SF4 6 x SF4
Ligand PC1 5 x PC1
Ligand FES 2 x FES
Ligand FMN 1 x FMN
Ligand K 1 x K
Ligand CDL 2 x CDL
Ligand GTP 1 x GTP
Ligand MG 1 x MG
Ligand NDP 1 x NDP
Ligand ZN 1 x ZN
Ligand EHZ 2 x EHZ
Ligand PGT 1 x PGT
Ligand MYR 1 x MYR
2 modified residues:
Ligand FME 7 x FME
Ligand SAC 1 x SAC

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-42174

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