› 4hea

X-ray diffraction
3.3Å resolution

Crystal structure of the entire respiratory complex I from Thermus thermophilus

Released:
DOI: 10.2210/pdb4hea/pdb
PDB entry 4hea coloured by chain, front view.
PDB entry 4hea coloured by chain, side view.
PDB entry 4hea coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Crystal structure of the entire respiratory complex I.
Baradaran R, Berrisford JM, Minhas GS, Sazanov LA
Nature 494 443-8 (2013)
PMID: 23417064

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-176328 (preferred)
Entry contents:
16 distinct polypeptide molecules
Macromolecules (16 distinct):
NADH-quinone oxidoreductase subunit 1 Chains: 1, B
Molecule details ›
Chains: 1, B
Length: 438 amino acids
Theoretical weight: 48.69 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56222 (Residues: 1-438; Coverage: 100%)
Gene names: TTHA0089, nqo1
Sequence domains:
Structure domains:
NADH-quinone oxidoreductase subunit 2 Chains: 2, C
Molecule details ›
Chains: 2, C
Length: 181 amino acids
Theoretical weight: 20.31 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56221 (Residues: 1-181; Coverage: 100%)
Gene names: TTHA0088, nqo2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
Structure domains:
NADH-quinone oxidoreductase subunit 3 Chains: 3, D
Molecule details ›
Chains: 3, D
Length: 783 amino acids
Theoretical weight: 86.66 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56223 (Residues: 1-783; Coverage: 100%)
Gene names: TTHA0090, nqo3
Sequence domains:
NADH-quinone oxidoreductase subunit 4 Chains: 4, E
Molecule details ›
Chains: 4, E
Length: 409 amino acids
Theoretical weight: 46.43 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56220 (Residues: 1-409; Coverage: 100%)
Gene names: TTHA0087, nqo4
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
Structure domains: Cytochrome-c3 Hydrogenase, chain B
NADH-quinone oxidoreductase subunit 5 Chains: 5, F
Molecule details ›
Chains: 5, F
Length: 207 amino acids
Theoretical weight: 23.89 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56219 (Residues: 1-207; Coverage: 100%)
Gene names: TTHA0086, nqo5
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NADH-quinone oxidoreductase subunit 6 Chains: 6, G
Molecule details ›
Chains: 6, G
Length: 181 amino acids
Theoretical weight: 20.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56218 (Residues: 1-181; Coverage: 100%)
Gene names: TTHA0085, nqo6
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
Structure domains: Rossmann fold
NADH-quinone oxidoreductase subunit 9 Chains: 9, O
Molecule details ›
Chains: 9, O
Length: 182 amino acids
Theoretical weight: 20.11 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56224 (Residues: 1-182; Coverage: 100%)
Gene names: TTHA0092, nqo9
Sequence domains: 4Fe-4S binding domain
Structure domains: Alpha-Beta Plaits
NADH-quinone oxidoreductase subunit 15 Chains: 7, I
Molecule details ›
Chains: 7, I
Length: 129 amino acids
Theoretical weight: 14.81 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKZ7 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA0496, nqo15
Sequence domains: NADH-quinone oxidoreductase chain 15
Structure domains: NADH-quinone oxidoreductase, subunit 15
Putative uncharacterized protein TTHA1528 Chains: W, X
Molecule details ›
Chains: W, X
Length: 131 amino acids
Theoretical weight: 14.2 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SI52 (Residues: 1-131; Coverage: 100%)
Gene name: TTHA1528
Sequence domains: Protein of unknown function (DUF3197)
Structure domains: TTHA1528-like
NADH-quinone oxidoreductase subunit 7 Chains: A, P
Molecule details ›
Chains: A, P
Length: 119 amino acids
Theoretical weight: 13.15 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56217 (Residues: 1-119; Coverage: 100%)
Gene names: TTHA0084, nqo7
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
Structure domains: NADH:ubiquinone/plastoquinone oxidoreductase, chain 3
NADH-quinone oxidoreductase subunit 10 Chains: J, R
Molecule details ›
Chains: J, R
Length: 176 amino acids
Theoretical weight: 18.56 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56225 (Residues: 1-176; Coverage: 100%)
Gene names: TTHA0093, nqo10
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
Structure domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ
NADH-quinone oxidoreductase subunit 11 Chains: K, S
Molecule details ›
Chains: K, S
Length: 95 amino acids
Theoretical weight: 10 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56226 (Residues: 1-95; Coverage: 100%)
Gene names: TTHA0094, nqo11
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
Structure domains: Helix Hairpins
NADH-quinone oxidoreductase subunit 12 Chains: L, T
Molecule details ›
Chains: L, T
Length: 606 amino acids
Theoretical weight: 65.19 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56227 (Residues: 1-606; Coverage: 100%)
Gene names: TTHA0095, nqo12
Sequence domains:
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
NADH-quinone oxidoreductase subunit 13 Chains: M, U
Molecule details ›
Chains: M, U
Length: 469 amino acids
Theoretical weight: 49.25 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56228 (Residues: 1-469; Coverage: 100%)
Gene names: TTHA0096, nqo13
Sequence domains: Proton-conducting membrane transporter
NADH-quinone oxidoreductase subunit 14 Chains: N, V
Molecule details ›
Chains: N, V
Length: 427 amino acids
Theoretical weight: 44.46 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56229 (Residues: 1-427; Coverage: 100%)
Gene names: TTHA0097, nqo14
Sequence domains: Proton-conducting membrane transporter
NADH-quinone oxidoreductase subunit 8 Chains: H, Q
Molecule details ›
Chains: H, Q
Length: 365 amino acids
Theoretical weight: 41.03 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q60019 (Residues: 1-365; Coverage: 100%)
Gene names: TTHA0091, nqo8
Sequence domains: NADH dehydrogenase

Ligands and Environments

3 bound ligands:
Ligand SF4 14 x SF4
Ligand FMN 2 x FMN
Ligand FES 4 x FES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 96.28Å b: 340.89Å c: 263.3Å
α: 90° β: 100.57° γ: 90°
R-values:
R R work R free
0.203 0.202 0.239

Quick links

Citations

99 review citations

Mitochondrial generation of superoxide and hydrogen peroxide as the source of mitochondrial redox signaling.
Brand MD. (2016)
98 more

77 mentions without citation

Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers.
Liu et al. (2014)
76 more