4HEA

Crystal structure of the entire respiratory complex I from Thermus thermophilus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 11, B438Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo1, TTHA0089
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 22, C181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo2, TTHA0088
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 33, D783Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo3, TTHA0090
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 44, E409Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo4, TTHA0087
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 55, F207Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo5, TTHA0086
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 66, G181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo6, TTHA0085
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 99, O182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo9, TTHA0092
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 157, I129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo15, TTHA0496
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein TTHA1528W, X131Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1528
Find proteins for Q5SI52 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 7A, P119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo7, TTHA0084
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 10J, R176Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo10, TTHA0093
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 11K, S95Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo11, TTHA0094
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 12L, T606Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo12, TTHA0095
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 13M, U469Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo13, TTHA0096
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 14N, V427Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo14, TTHA0097
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit 8H, Q365Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo8, TTHA0091
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc		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))
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN
Download CCD File 
1, B
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
SF4
Query on SF4
Download CCD File 
1, 3, 6, 9, B, D, G, O
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
FES
Query on FES
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: 3.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.28α = 90
b = 340.89β = 100.57
c = 263.3γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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