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 

Starting Models: experimental
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This is version 1.3 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 1A [auth 1],
Q [auth B]
438Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 2B [auth 2],
R [auth C]
181Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 3C [auth 3],
S [auth D]
783Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 4D [auth 4],
T [auth E]
409Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 5E [auth 5],
U [auth F]
207Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 6F [auth 6],
V [auth G]
181Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 9G [auth 9],
W [auth O]
182Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 15H [auth 7],
X [auth I]
129Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein TTHA1528I [auth W],
Y [auth X]
131Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 7J [auth A],
Z [auth P]
119Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 10AA [auth R],
K [auth J]
176Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 11BA [auth S],
L [auth K]
95Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 12CA [auth T],
M [auth L]
606Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 13DA [auth U],
N [auth M]
469Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 14EA [auth V],
O [auth N]
427Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 8FA [auth Q],
P [auth H]
365Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 3 Unique
IDChains Name / 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
SF4
Query on SF4

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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-UHFFFAOYSA-N
FES
Query on FES

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IA [auth 2],
MA [auth 3],
SA [auth C],
WA [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
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  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-03-13
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary