3M9S

Crystal structure of respiratory complex I from Thermus thermophilus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The architecture of respiratory complex I

Efremov, R.G., Baradaran, R., Sazanov, L.A.

(2010) Nature 465: 441-445

  • DOI: https://doi.org/10.1038/nature09066
  • Primary Citation of Related Structures:  
    3M9C, 3M9S

  • PubMed Abstract: 

    • Complex I is the first enzyme of the respiratory chain and has a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation by an unknown mechanism. Dysfunction of complex I has been implicated in many human neurodegenerative diseases ...

    Complex I is the first enzyme of the respiratory chain and has a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation by an unknown mechanism. Dysfunction of complex I has been implicated in many human neurodegenerative diseases. We have determined the structure of its hydrophilic domain previously. Here, we report the alpha-helical structure of the membrane domain of complex I from Escherichia coli at 3.9 A resolution. The antiporter-like subunits NuoL/M/N each contain 14 conserved transmembrane (TM) helices. Two of them are discontinuous, as in some transporters. Unexpectedly, subunit NuoL also contains a 110-A long amphipathic alpha-helix, spanning almost the entire length of the domain. Furthermore, we have determined the structure of the entire complex I from Thermus thermophilus at 4.5 A resolution. The L-shaped assembly consists of the alpha-helical model for the membrane domain, with 63 TM helices, and the known structure of the hydrophilic domain. The architecture of the complex provides strong clues about the coupling mechanism: the conformational changes at the interface of the two main domains may drive the long amphipathic alpha-helix of NuoL in a piston-like motion, tilting nearby discontinuous TM helices, resulting in proton translocation.

    Organizational Affiliation: 

    Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 1A [auth 1],
N [auth A]		438Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo1, TTHA0089
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 2B [auth 2],
O [auth B]		181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo2, TTHA0088
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 3C [auth 3],
P [auth C]		783Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo3, TTHA0090
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 4D [auth 4],
Q [auth D]		409Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo4, TTHA0087
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit CE [auth 5],
R [auth E]		207Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo5, TTHA0086
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit BF [auth 6],
S [auth F]		181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo6, TTHA0085
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit IG [auth 9],
T [auth G]		182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo9, TTHA0092
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 15H [auth 7],
U [auth J]		129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo15, TTHA0496
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 12I [auth L],
V [auth O]		469Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 13J [auth M],
W [auth P]		392Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 14K [auth N],
X [auth Q]		379Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunits 7, 10 and 11L [auth R],
Y [auth S]		274Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 8M [auth H],
Z [auth T]		181Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN
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BA [auth 1],
LA [auth A]		FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
SF4
Query on SF4
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AA [auth 1]
DA [auth 3]
EA [auth 3]
FA [auth 3]
HA [auth 6]
AA [auth 1],
DA [auth 3],
EA [auth 3],
FA [auth 3],
HA [auth 6],
IA [auth 9],
JA [auth 9],
KA [auth A],
NA [auth C],
OA [auth C],
PA [auth C],
RA [auth F],
SA [auth G],
TA [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
FES
Query on FES
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CA [auth 2],
GA [auth 3],
MA [auth B],
QA [auth C]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.39α = 90
b = 336.09β = 100.59
c = 262.24γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description