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Crystal structure of the membrane domain of respiratory complex I from Thermus thermophilus

X-ray diffraction
3.3Å resolution
PDB entry 4he8 coloured by chain, front view.
PDB entry 4he8 coloured by chain, side view.
PDB entry 4he8 coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Assembly composition:
hetero heptamer (preferred)
Entry contents: 7 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: NADH-quinone oxidoreductase
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Multimeric state: hetero heptamer
Accessible surface area: 67162.43 Å2
Buried surface area: 36885.19 Å2
Dissociation area: 3,474.53 Å2
Dissociation energy (ΔGdiss): 64.73 kcal/mol
Dissociation entropy (TΔSdiss): 16.23 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-176330
Assembly 2
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Assembly Name: NADH-quinone oxidoreductase
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Multimeric state: hetero heptamer
Accessible surface area: 67242.39 Å2
Buried surface area: 36773.66 Å2
Dissociation area: 3,478.43 Å2
Dissociation energy (ΔGdiss): 63.82 kcal/mol
Dissociation entropy (TΔSdiss): 16.23 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-176330

Macromolecules

NADH-quinone oxidoreductase subunit 7
Chains: A, B
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
Pfam: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
InterPro:
CATH: NADH:ubiquinone/plastoquinone oxidoreductase, chain 3
NADH-quinone oxidoreductase subunit 7 in PDB entry 4he8, assembly 1, front view.
NADH-quinone oxidoreductase subunit 7 in PDB entry 4he8, assembly 1, side view.
NADH-quinone oxidoreductase subunit 7 in PDB entry 4he8, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q56217  
1119102030405060708090100110
 
50100MAPIQEYVGTLIYVGVALFIGVAALLVGALLGPKKPGRAKLMPYESGNDPAGEVKRFPVHFYVVAMLFILFDVEVAFLWPYAVSAGGLGLYGFLGVLAFTLLLFVGFLYEWWKGVMRWH
UniProt
Q56217
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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NADH-quinone oxidoreductase subunit 10
Chains: D, J
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
Pfam: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
InterPro:
CATH: NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ
NADH-quinone oxidoreductase subunit 10 in PDB entry 4he8, assembly 1, front view.
NADH-quinone oxidoreductase subunit 10 in PDB entry 4he8, assembly 1, side view.
NADH-quinone oxidoreductase subunit 10 in PDB entry 4he8, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q56225  
117620406080100120140160
 
50100150MSLLEGLALFLLLLSGVLVVTLRNAIHAALALILNFLVLAGVYVALDARFLGFIQVIVYAGAIVVLFLFVIMLLFAAQGEIGFDPLVRSRPLAALLALGVAGILAAGLWGLDLAFTQDLKGGLPQALGPLLYGDWLFVLLAVGFLLMAATVVAVALVEPGKASRAKEAEKREEVAR
UniProt
Q56225
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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NADH-quinone oxidoreductase subunit 11
Chains: E, K
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
Pfam: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
InterPro:
CATH: Helix Hairpins
NADH-quinone oxidoreductase subunit 11 in PDB entry 4he8, assembly 1, front view.
NADH-quinone oxidoreductase subunit 11 in PDB entry 4he8, assembly 1, side view.
NADH-quinone oxidoreductase subunit 11 in PDB entry 4he8, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q56226  
195102030405060708090
 
50MSYLLTSALLFALGVYGVLTRRTAILVFLSIELMLNAANLSLVGFARAYGLDGQVAALMVIAVAAAEVAVGLGLIVAIFRHRESTAVDDLSELRG
UniProt
Q56226
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Interaction interfaces
Sequence conservation
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NADH-quinone oxidoreductase subunit 12
Chains: F, L
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
Pfam:
InterPro:
CATH: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
NADH-quinone oxidoreductase subunit 12 in PDB entry 4he8, assembly 1, front view.
NADH-quinone oxidoreductase subunit 12 in PDB entry 4he8, assembly 1, side view.
NADH-quinone oxidoreductase subunit 12 in PDB entry 4he8, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q56227  
160650100150200250300350400450500550600
 
200400600MALLGTILLPLLGFALLGLFGKRMREPLPGVLASGLVLASFLLGAGLLLSGGARFQAEWLPGIPFSLLLDNLSGFMLLIVTGVGFLIHVYAIGYMGGDPGYSRFFAYFNLFIAMMLTLVLADSYPVMFIGWEGVGLASFLLIGFWYKNPQYADSARKAFIVNRIGDLGFMLGMAILWALYGTLSISELKEAMEGPLKNPDLLALAGLLLFLGAVGKSAQIPLMVWLPDAMAGPTPVSALIHAATMVTAGVYLIARSSFLYSVLPDVSYAIAVVGLLTAAYGALSAFGQTDIKKIVAYSTISQLGYMFLAAGVGAYWVALFHVFTHAFFKALLFLASGSVIHALGGEQDVRKMGGLWKHLPQTRWHALIGALALGGLPLLSGFWSKDAILAATLTYPFGGVGFYVGALLVAVLTAMYAMRWFVLVFLGEERGHHHPHEAPPVMLWPNHLLALGSVLAGYLALPHPLPNVLEPFLKPALAEVEAHHLSLGAEWGLIALSAAVALLGLWAGFVFFQRKVFPAWYLAFEAASREAFYVDRAYNALIVNPLKALAEALFYGDRGLLSGYFGLGGAARSLGQGLARLQTGYLRVYALLFVLGALLLLGVMRW
UniProt
Q56227
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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NADH-quinone oxidoreductase subunit 13
Chains: G, M
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
Pfam: Proton-conducting membrane transporter
InterPro:
NADH-quinone oxidoreductase subunit 13 in PDB entry 4he8, assembly 1, front view.
NADH-quinone oxidoreductase subunit 13 in PDB entry 4he8, assembly 1, side view.
NADH-quinone oxidoreductase subunit 13 in PDB entry 4he8, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q56228  
146950100150200250300350400450
 
200400MVVLAVLLPVVFGALLLLGLPRALGVLGAGLSFLLNLYLFLTHPGGVAHAFQAPLLPGAGVYWAFGLDGLSALFFLTIALTVFLGALVARVEGRFLGLALLMEGLLLGLFAARDLLVFYVFFEAALIPALLMLYLYGGEGRTRALYTFVLFTLVGSLPMLAAVLGARLLSGSPTFLLEDLLAHPLQEEAAFWVFLGFALAFAIKTPLFPLHAWLPPFHQENHPSGLADALGTLYKVGVFAFFRFAIPLAPEGFAQAQGLLLFLAALSALYGAWVAFAAKDFKTLLAYAGLSHMGVAALGVFSGTPEGAMGGLYLLAASGVYTGGLFLLAGRLYERTGTLEIGRYRGLAQSAPGLAALALILFLAMVGLPGLSGFPGEFLTLLGAYKASPWLAALAFLSVIASAAYALTAFQKTFWEEGGSGVKDLAGAEWGFALLSVLALLLMGVFPGYFARGLHPLAEAFAKLLGGGA
UniProt
Q56228
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
Molecule details ›

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NADH-quinone oxidoreductase subunit 14
Chains: I, N
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
Pfam: Proton-conducting membrane transporter
InterPro:
NADH-quinone oxidoreductase subunit 14 in PDB entry 4he8, assembly 1, front view.
NADH-quinone oxidoreductase subunit 14 in PDB entry 4he8, assembly 1, side view.
NADH-quinone oxidoreductase subunit 14 in PDB entry 4he8, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q56229  
142750100150200250300350400
 
200400MTLAILAVFSVALTLLGFVLPPQGVKRATLLGLALALASLLLTWGKPFAFGPYAVDGVSQVFTLLALLGALWTVGLVRSGRFEFYLLVLYAALGMHLLASTRHLLLMLVALEALSLPLYALATWRRGQGLEAALKYFLLGALAAAFFLYGAALFYGATGSLVLGAPGEGPLYALALGLLLVGLGFKAALAPFHFWTPDVYQGSPTPVVLFMATSVKAAAFAALLRVAAPPEALALLVALSVVVGNLAALAQKEAKRLLAYSSIAHAGYMALALYTGNAQALGFYLLTYVLATGLAFAVLSQISPDRVPLEALRGLYRKDPLLGLAFLVAMLSLLGLPPLAGFWGKYLAFAEAARAGAWGVLVLALVTSAVSAYYYLGLGLAVFARPEETPFRPGPPWARAAVVAAGVLLLALGLLPGLVLPALAAGG
UniProt
Q56229
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
Molecule details ›

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NADH-quinone oxidoreductase subunit 8
Chains: C, H
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
Pfam: NADH dehydrogenase
InterPro:
NADH-quinone oxidoreductase subunit 8 in PDB entry 4he8, assembly 1, front view.
NADH-quinone oxidoreductase subunit 8 in PDB entry 4he8, assembly 1, side view.
NADH-quinone oxidoreductase subunit 8 in PDB entry 4he8, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q60019  
136550100150200250300350
 
100200300MTWSYPVDPYWMVALKALLVVVGLLTAFAFMTLIERRLLARFQVRMGPNRVGPFGLLQPLADAIKSIFKEDIVVAQADRFLFVLAPLISVVFALLAFGLIPFGPPGSFFGYQPWVINLDLGILYLFAVSELAVYGIFLSGWASGSKYSLLGSLRSSASLISYELGLGLALLAPVLLVGSLNLNDIVNWQKEHGWLFLYAFPAFLVYLIASMAEAARTPFDLPEAEQELVGGYHTEYSSIKWALFQMAEYIHFITASALIPTLFLGGWTMPVLEVPYLWMFLKIAFFLFFFIWIRATWFRLRYDQLLRFGWGFLFPLALLWFLVTALVVALDLPRTYLLYLSALSFLVLLGAVLYTPKPARKGGGA
UniProt
Q60019
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Interaction interfaces
Sequence conservation
Molecule details ›

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