4HEA

Crystal structure of the entire respiratory complex I from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3027 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the entire respiratory complex I.

Baradaran, R.Berrisford, J.M.Minhas, G.S.Sazanov, L.A.

(2013) Nature 494: 443-448

  • DOI: 10.1038/nature11871
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neur ...

    Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.


    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, B
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, C
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, D
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, E
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 5
5, F
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 6
6, G
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 9
9, O
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, I
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
Putative uncharacterized protein TTHA1528
W, X
131Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I complete
Find proteins for Q5SI52 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SI52
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 7
A, P
119Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo7
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 Q56217 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56217
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 10
J, R
176Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo10
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 Q56225 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56225
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 11
K, S
95Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo11
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 Q56226 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56226
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 12
L, T
606Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo12
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 Q56227 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56227
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 13
M, U
469Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo13
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 Q56228 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56228
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 14
N, V
427Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo14
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 Q56229 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56229
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 8
H, Q
365Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: nqo8
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 Q60019 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q60019
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, B, D, G, O
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
1, B
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, C, D
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3027 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 96.280α = 90.00
b = 340.890β = 100.57
c = 263.300γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-03-13
    Type: Database references