3M9S

Crystal structure of respiratory complex I from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/nature09066
  • Primary Citation of Related Structures:  

  • 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 implic ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 1
1, A
438Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo1
EC: 1.6.5.11
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I complete
Find proteins for Q56222 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56222
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 2
2, B
181Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo2
EC: 1.6.5.11
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I complete
Find proteins for Q56221 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56221
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 3
3, C
783Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo3
EC: 1.6.5.11
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I complete
Find proteins for Q56223 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56223
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 4
4, D
409Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo4
EC: 1.6.5.11
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I complete
Find proteins for Q56220 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56220
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit C
5, E
207Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo5
EC: 1.6.5.11
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I complete
Find proteins for Q56219 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56219
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit B
6, F
181Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo6
EC: 1.6.5.11
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I complete
Find proteins for Q56218 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56218
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit I
9, G
182Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo9
EC: 1.6.5.11
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I complete
Find proteins for Q56224 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56224
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 15
7, J
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo15
EC: 1.6.5.11
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I complete
Find proteins for Q5SKZ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKZ7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 12
L, O
469N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 13
M, P
392N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 14
N, Q
379N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunits 7, 10 and 11
R, S
274N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 8
H, T
181N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
1, 3, 6, 9, A, C, F, G
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
1, A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
2, 3, B, C
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
H, L, M, N, O, P, Q, R, S, T
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 96.390α = 90.00
b = 336.090β = 100.59
c = 262.240γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance