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 

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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:  
    4HEA, 4HE8

  • 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: nqo1TTHA0089
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: nqo2TTHA0088
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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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: nqo3TTHA0090
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: nqo4TTHA0087
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
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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: nqo5TTHA0086
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: nqo6TTHA0085
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
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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: nqo9TTHA0092
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: nqo15TTHA0496
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: nqo7TTHA0084
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: nqo10TTHA0093
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: nqo11TTHA0094
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: nqo12TTHA0095
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: nqo13TTHA0096
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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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: nqo14TTHA0097
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: nqo8TTHA0091
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
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] , OA [auth 9] , PA [auth 9] , QA [auth B] , 
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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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