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
  • Primary Citation of Related Structures:  
    4HE8, 4HEA

  • 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 neurodegenerative diseases ...

    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 LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 1A [auth 1],
Q [auth B]		438Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo1, TTHA0089
EC: 1.6.5.3 (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],
R [auth C]		181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo2, TTHA0088
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 3C [auth 3],
S [auth D]		783Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo3, TTHA0090
EC: 1.6.5.3 (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],
T [auth E]		409Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo4, TTHA0087
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 5E [auth 5],
U [auth F]		207Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo5, TTHA0086
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 6F [auth 6],
V [auth G]		181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo6, TTHA0085
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 9G [auth 9],
W [auth O]		182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo9, TTHA0092
EC: 1.6.5.3 (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],
X [auth I]		129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo15, TTHA0496
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized protein TTHA1528I [auth W],
Y [auth X]		131Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1528
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 7J [auth A],
Z [auth P]		119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo7, TTHA0084
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 10K [auth J],
AA [auth R]		176Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo10, TTHA0093
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 11L [auth K],
BA [auth S]		95Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo11, TTHA0094
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 12M [auth L],
CA [auth T]		606Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo12, TTHA0095
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 13N [auth M],
DA [auth U]		469Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo13, TTHA0096
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 14O [auth N],
EA [auth V]		427Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo14, TTHA0097
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 8P [auth H],
FA [auth Q]		365Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo8, TTHA0091
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN
Download Ideal Coordinates CCD File 
HA [auth 1],
RA [auth B]		FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
GA [auth 1],
JA [auth 3],
KA [auth 3],
LA [auth 3],
NA [auth 6],
GA [auth 1],
JA [auth 3],
KA [auth 3],
LA [auth 3],
NA [auth 6],
OA [auth 9],
PA [auth 9],
QA [auth B],
TA [auth D],
UA [auth D],
VA [auth D],
XA [auth G],
YA [auth O],
ZA [auth O]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
FES
Query on FES
Download Ideal Coordinates CCD File 
IA [auth 2],
MA [auth 3],
SA [auth C],
WA [auth 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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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

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