› 7zmb

Electron Microscopy
2.75Å resolution

CryoEM structure of mitochondrial complex I from Chaetomium thermophilum (state 2)

Released:
DOI: 10.2210/pdb7zmb/pdb
PDB entry 7zmb coloured by chain, front view.
PDB entry 7zmb coloured by chain, side view.
PDB entry 7zmb coloured by chain, top view.
Source organism: Thermochaetoides thermophila DSM 1495
Primary publication:
Conformational changes in mitochondrial complex I of the thermophilic eukaryote Chaetomium thermophilum.
Laube E, Meier-Credo J, Langer JD, Kühlbrandt W
Sci Adv 8 eadc9952 (2022)
PMID: 36427319
Related structures: EMD-14794

Function and Biology Details

Reactions catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 43-mer (preferred)
PDBe Complex ID:
PDB-CPX-123873 (preferred)
Entry contents:
42 distinct polypeptide molecules
Macromolecules (42 distinct):
NADH-ubiquinone oxidoreductase chain 1 Chain: 1
Molecule details ›
Chain: 1
Length: 378 amino acids
Theoretical weight: 41.72 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G1DJA6 (Residues: 1-378; Coverage: 100%)
Gene name: CTHT_m000470
Sequence domains: NADH dehydrogenase
NADH-ubiquinone oxidoreductase chain 2 Chain: 2
Molecule details ›
Chain: 2
Length: 571 amino acids
Theoretical weight: 64.13 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G1DJ98 (Residues: 1-571; Coverage: 100%)
Gene name: CTHT_m000270
Sequence domains: Proton-conducting membrane transporter
NADH-ubiquinone oxidoreductase chain 3 Chain: 3
Molecule details ›
Chain: 3
Length: 146 amino acids
Theoretical weight: 16.33 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G1DJ99 (Residues: 1-146; Coverage: 100%)
Gene name: CTHT_m000280
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH-ubiquinone oxidoreductase chain 4 Chain: 4
Molecule details ›
Chain: 4
Length: 542 amino acids
Theoretical weight: 60.81 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G1DJA7 (Residues: 1-542; Coverage: 100%)
Gene name: CTHT_m000480
Sequence domains: Proton-conducting membrane transporter
NADH-ubiquinone oxidoreductase chain 5 Chain: 5
Molecule details ›
Chain: 5
Length: 679 amino acids
Theoretical weight: 75.87 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G1DJA3 (Residues: 1-444, 445-665; Coverage: 100%)
Gene name: CTHT_m000370
Sequence domains:
NADH-ubiquinone oxidoreductase chain 6 Chain: 6
Molecule details ›
Chain: 6
Length: 224 amino acids
Theoretical weight: 24.82 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G1DJ96 (Residues: 1-224; Coverage: 100%)
Gene name: CTHT_m000070
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: 8
Molecule details ›
Chain: 8
Length: 86 amino acids
Theoretical weight: 10.31 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SAE9 (Residues: 1-86; Coverage: 100%)
Gene name: CTHT_0042030
Sequence domains: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7)
Subunit NDUFS5 of NADH-ubiquinone oxidoreductase (Complex I) Chain: 9
Molecule details ›
Chain: 9
Length: 785 amino acids
Theoretical weight: 87.14 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SG48 (Residues: 1-99, 100-784; Coverage: 100%)
Gene name: CTHT_0065020
NADH-ubiquinone oxidoreductase-like protein Chain: A
Molecule details ›
Chain: A
Length: 749 amino acids
Theoretical weight: 82.1 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RYA1 (Residues: 1-750; Coverage: 100%)
Gene name: CTHT_0005960
Sequence domains:
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 507 amino acids
Theoretical weight: 55.45 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SA46 (Residues: 1-507; Coverage: 100%)
Gene name: CTHT_0040970
Sequence domains:
NADH-quinone oxidoreductase subunit D domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 499 amino acids
Theoretical weight: 55.91 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SCG0 (Residues: 1-506; Coverage: 99%)
Gene name: CTHT_0057080
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I) Chain: D
Molecule details ›
Chain: D
Length: 86 amino acids
Theoretical weight: 9.83 KDa
Source organism: Thermochaetoides thermophila DSM 1495
NAD-dependent epimerase/dehydratase domain-containing protein Chain: E
Molecule details ›
Chain: E
Length: 378 amino acids
Theoretical weight: 43.8 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SB35 (Residues: 1-102, 103-224, 225-368; Coverage: 100%)
Gene name: CTHT_0048740
Sequence domains: NAD dependent epimerase/dehydratase family
NADH-ubiquinone oxidoreductase-like protein Chain: F
Molecule details ›
Chain: F
Length: 261 amino acids
Theoretical weight: 29.24 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S8H4 (Residues: 1-261; Coverage: 100%)
Gene name: CTHT_0029890
Sequence domains: ETC complex I subunit conserved region
NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein Chain: G
Molecule details ›
Chain: G
Length: 293 amino acids
Theoretical weight: 33.38 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S8U1 (Residues: 1-293; Coverage: 100%)
Gene name: CTHT_0043400
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NADH-ubiquinone oxidoreductase-like protein Chain: H
Molecule details ›
Chain: H
Length: 318 amino acids
Theoretical weight: 35.01 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SDM6 (Residues: 1-318; Coverage: 100%)
Gene name: CTHT_0052320
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
4Fe-4S ferredoxin-type domain-containing protein Chain: I
Molecule details ›
Chain: I
Length: 223 amino acids
Theoretical weight: 25.42 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SBG8 (Residues: 661-883; Coverage: 25%)
Gene name: CTHT_0050220
Sequence domains: 4Fe-4S dicluster domain
NADH-ubiquinone oxidoreductase-like protein Chain: J
Molecule details ›
Chain: J
Length: 199 amino acids
Theoretical weight: 21.61 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S2B3 (Residues: 1-199; Coverage: 100%)
Gene name: CTHT_0016630
NADH:ubiquinone oxidoreductase-like 20kDa subunit domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 230 amino acids
Theoretical weight: 25.55 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S9I6 (Residues: 1-230; Coverage: 100%)
Gene name: CTHT_0046020
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH-ubiquinone oxidoreductase chain 4L Chain: L
Molecule details ›
Chain: L
Length: 89 amino acids
Theoretical weight: 9.84 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G1DJA2 (Residues: 1-89; Coverage: 100%)
Gene name: CTHT_m000360
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
Zinc finger CHCC-type domain-containing protein Chain: M
Molecule details ›
Chain: M
Length: 168 amino acids
Theoretical weight: 18.61 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S6J1 (Residues: 1-149; Coverage: 84%)
Gene name: CTHT_0026400
Sequence domains: Zinc-finger domain
Acyl carrier protein Chains: O, Q
Molecule details ›
Chains: O, Q
Length: 141 amino acids
Theoretical weight: 15.59 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SBG9 (Residues: 1-141; Coverage: 100%)
Gene name: CTHT_0050230
Sequence domains: Phosphopantetheine attachment site
NADH-ubiquinone oxidoreductase B14 subunit-like protein Chain: P
Molecule details ›
Chain: P
Length: 124 amino acids
Theoretical weight: 14.84 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S4Q3 (Residues: 1-124; Coverage: 100%)
Gene name: CTHT_0023140
Sequence domains: Complex1_LYR-like
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: R
Molecule details ›
Chain: R
Length: 99 amino acids
Theoretical weight: 11.64 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SAY0 (Residues: 1-99; Coverage: 100%)
Gene name: CTHT_0048190
Sequence domains: Complex 1 protein (LYR family)
DNA replication ATP-dependent helicase/nuclease DNA2 Chain: S
Molecule details ›
Chain: S
Length: 143 amino acids
Theoretical weight: 15.85 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SAN0 (Residues: 1706-1848; Coverage: 8%)
Gene name: CTHT_0042860
Sequence domains: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I)
NADH-ubiquinone oxidoreductase Chain: U
Molecule details ›
Chain: U
Length: 186 amino acids
Theoretical weight: 21.52 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S0R3 (Residues: 1-186; Coverage: 100%)
Gene name: CTHT_0010950
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: W
Molecule details ›
Chain: W
Length: 121 amino acids
Theoretical weight: 14.04 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SB83 (Residues: 1-121; Coverage: 100%)
Gene name: CTHT_0049240
Sequence domains: GRIM-19 protein
NADH-ubiquinone oxidoreductase-like protein Chain: X
Molecule details ›
Chain: X
Length: 191 amino acids
Theoretical weight: 21.65 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S0S8 (Residues: 1-191; Coverage: 100%)
Gene name: CTHT_0011100
Sequence domains:
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: Y
Molecule details ›
Chain: Y
Length: 210 amino acids
Theoretical weight: 23.49 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S3Y7 (Residues: 1-210; Coverage: 100%)
Gene name: CTHT_0039340
Sequence domains: NADH dehydrogenase ubiquinone Fe-S protein 4
NADH-ubiquinone oxidoreductase-like protein Chain: Z
Molecule details ›
Chain: Z
Length: 196 amino acids
Theoretical weight: 21.16 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SEF0 (Residues: 1-188; Coverage: 100%)
Gene name: CTHT_0063510
NADH dehydrogenase (Ubiquinone)-like protein Chain: a
Molecule details ›
Chain: a
Length: 203 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RXU4 (Residues: 1-209; Coverage: 25%)
Gene name: CTHT_0000410
Sequence domains: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8)
Subunit NDUFC2 of NADH-ubiquinone oxidoreductase (Complex I) Chain: b
Molecule details ›
Chain: b
Length: 94 amino acids
Theoretical weight: 10.82 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S812 (Residues: 1-94; Coverage: 100%)
Gene name: CTHT_0028990
Subunit NDUFB3 of NADH-ubiquinone oxidoreductase (Complex I) Chain: c
Molecule details ›
Chain: c
Length: 93 amino acids
Theoretical weight: 11.15 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S681 (Residues: 1-93; Coverage: 100%)
Gene name: CTHT_0025810
Sequence domains: NADH-ubiquinone oxidoreductase B12 subunit family
NADH-ubiquinone oxidoreductase-like protein Chain: d
Molecule details ›
Chain: d
Length: 105 amino acids
Theoretical weight: 12.51 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SEZ1 (Residues: 1-105; Coverage: 100%)
Gene name: CTHT_0060200
Subunit NDUFB2 of NADH-ubiquinone oxidoreductase (Complex I) Chain: e
Molecule details ›
Chain: e
Length: 46 amino acids
Theoretical weight: 5.28 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Ribosomal protein/NADH dehydrogenase domain-containing protein Chain: f
Molecule details ›
Chain: f
Length: 95 amino acids
Theoretical weight: 10.9 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S1P3 (Residues: 1-96; Coverage: 99%)
Gene name: CTHT_0014320
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
NADH-ubiquinone oxidoreductase 9.5 kDa subunit Chain: g
Molecule details ›
Chain: g
Length: 82 amino acids
Theoretical weight: 9.08 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RZZ2 (Residues: 1-82; Coverage: 100%)
Gene name: CTHT_0008140
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit Chain: h
Molecule details ›
Chain: h
Length: 134 amino acids
Theoretical weight: 15.97 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S775 (Residues: 118-251; Coverage: 53%)
Gene name: CTHT_0027690
Sequence domains: NADH ubiquinone oxidoreductase subunit NDUFA12
Subunit NDUFB6 of NADH-ubiquinone oxidoreductase (Complex I) Chain: i
Molecule details ›
Chain: i
Length: 93 amino acids
Theoretical weight: 10.86 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S569 (Residues: 1-93; Coverage: 100%)
Gene name: CTHT_0032450
NADH-ubiquinone oxidoreductase B15 subunit Chain: j
Molecule details ›
Chain: j
Length: 75 amino acids
Theoretical weight: 8.76 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S5C8 (Residues: 1-75; Coverage: 100%)
Gene name: CTHT_0024350
NADH-ubiquinone oxidoreductase-like protein Chain: n
Molecule details ›
Chain: n
Length: 184 amino acids
Theoretical weight: 20.82 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S086 (Residues: 16-147; Coverage: 90%)
Gene name: CTHT_0009140
Oxidoreductase-like domain-containing protein Chain: o
Molecule details ›
Chain: o
Length: 380 amino acids
Theoretical weight: 41.61 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S982 (Residues: 1-380; Coverage: 100%)
Gene name: CTHT_0044890
Sequence domains: Oxidoreductase-like protein, N-terminal

Ligands and Environments

10 bound ligands:
Ligand 3PE 17 x 3PE
Ligand PC1 8 x PC1
Ligand CDL 5 x CDL
Ligand LMN 3 x LMN
Ligand FES 2 x FES
Ligand SF4 6 x SF4
Ligand FMN 1 x FMN
Ligand NDP 1 x NDP
Ligand ZN 1 x ZN
Ligand ZMP 2 x ZMP
1 modified residue:
Ligand 2MR 1 x 2MR

Experiments and Validation Details

Entry percentile scores
Resolution: 2.75Å
Relevant EMDB volumes: EMD-14794

Quick links

Citations

3 review citations

The biogenesis and regulation of the plant oxidative phosphorylation system.
Ghifari et al. (2023)
2 more

2 mentions without citation

Investigation of hydrated channels and proton pathways in a high-resolution cryo-EM structure of mammalian complex I.
Grba et al. (2023)
1 more