3I9V

Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 2 mol/ASU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the mechanism of respiratory complex I

Berrisford, J.M.Sazanov, L.A.

(2009) J.Biol.Chem. 284: 29773-29783

  • DOI: 10.1074/jbc.M109.032144
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source o ...

    Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source of reactive oxygen species, which may be one of the causes of aging. Dysfunction of complex I is implicated in many human neurodegenerative diseases. We have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 A resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of reactive oxygen species production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide-binding pocket, as well as small but significant shifts of several alpha-helices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby iron-sulfur clusters N2 and N6a/b. Cluster N2 is the electron donor to quinone and is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines.


    Related Citations: 
    • Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus
      Sazanov, L.A.,Hinchliffe, P.
      (2006) Science 311: 1430


    Organizational Affiliation

    Medical Research Council Mitochondrial Biology Unit, Cambridge CB20XY, United Kingdom.




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: 7.1.1.-
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: 7.1.1.-
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: 7.1.1.-
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: 7.1.1.-
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 5
5, E
207Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo5
EC: 7.1.1.-
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 6
6, F
181Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo6
EC: 7.1.1.-
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 9
9, G
182Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo9
EC: 7.1.1.-
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, H
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo15
EC: 7.1.1.-
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
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
2, 3, 4, 5, 7, C, D, E, H
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
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
CA
Query on CA

Download SDF File 
Download CCD File 
3, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 108.963α = 90.00
b = 150.514β = 92.19
c = 216.726γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance