2FUG

Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 

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Literature

Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus.

Sazanov, L.A., Hinchliffe, P.

(2006) Science 311: 1430-1436

  • DOI: https://doi.org/10.1126/science.1123809
  • Primary Citation of Related Structures:  
    2FUG

  • PubMed Abstract: 

    • Respiratory complex I plays a central role in cellular energy production in bacteria and mitochondria. Its dysfunction is implicated in many human neurodegenerative diseases, as well as in aging. The crystal structure of the hydrophilic domain (peripheral arm) of complex I from Thermus thermophilus has been solved at 3 ...

    Respiratory complex I plays a central role in cellular energy production in bacteria and mitochondria. Its dysfunction is implicated in many human neurodegenerative diseases, as well as in aging. The crystal structure of the hydrophilic domain (peripheral arm) of complex I from Thermus thermophilus has been solved at 3.3 angstrom resolution. This subcomplex consists of eight subunits and contains all the redox centers of the enzyme, including nine iron-sulfur clusters. The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway, and of the distal cluster N1a, a possible antioxidant. The structure reveals new aspects of the mechanism and evolution of the enzyme. The terminal cluster N2 is coordinated, uniquely, by two consecutive cysteines. The novel subunit Nqo15 has a similar fold to the mitochondrial iron chaperone frataxin, and it may be involved in iron-sulfur cluster regeneration in the complex.

    Related Citations: 
    • Organization of iron-sulfur clusters in respiratory complex I
      Hinchliffe, P., Sazanov, L.A.
      (2005) Science 309: 771
    Organizational Affiliation: 

    Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, U.K. sazanov@mrc-dunn.cam.ac.uk



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase chain 1A [auth 1],
I [auth A],
Q [auth J],
Y [auth S]		438Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo1, TTHA0089
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q56222 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity Groups  
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UniProt GroupQ56222
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase chain 2B [auth 2],
J [auth B],
R [auth K],
Z [auth T]		181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo2, TTHA0088
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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UniProt GroupQ56221
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase chain 3AA [auth U],
C [auth 3],
K [auth C],
S [auth L]		783Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo3, TTHA0090
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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UniProt GroupQ56223
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase chain 4BA [auth V],
D [auth 4],
L [auth D],
T [auth M]		409Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo4, TTHA0087
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase chain 5CA [auth W],
E [auth 5],
M [auth E],
U [auth N]		207Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo5, TTHA0086
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase chain 6DA [auth X],
F [auth 6],
N [auth F],
V [auth O]		181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo6, TTHA0085
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase chain 9EA [auth Y],
G [auth 9],
O [auth G],
W [auth P]		182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo9, TTHA0092
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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UniProt GroupQ56224
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
conserved hypothetical proteinFA [auth Z],
H [auth 7],
P [auth H],
X [auth Q]		129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo15, TTHA0496
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q5SKZ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SKZ7
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN
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JB [auth Q],
PA [auth 7],
TB [auth Z],
ZA [auth H]		FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
SF4
Query on SF4
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AB [auth J]
CB [auth L]
DB [auth L]
EB [auth L]
GA [auth 1]
AB [auth J],
CB [auth L],
DB [auth L],
EB [auth L],
GA [auth 1],
GB [auth O],
HB [auth P],
IA [auth 3],
IB [auth P],
JA [auth 3],
KA [auth 3],
KB [auth S],
MA [auth 6],
MB [auth U],
NA [auth 9],
NB [auth U],
OA [auth 9],
OB [auth U],
QA [auth A],
QB [auth X],
RB [auth Y],
SA [auth C],
SB [auth Y],
TA [auth C],
UA [auth C],
WA [auth F],
XA [auth G],
YA [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
FES
Query on FES
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BB [auth K]
FB [auth L]
HA [auth 2]
LA [auth 3]
LB [auth T]
BB [auth K],
FB [auth L],
HA [auth 2],
LA [auth 3],
LB [auth T],
PB [auth U],
RA [auth B],
VA [auth C]
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: 0.298 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.08α = 90
b = 266.112β = 104.71
c = 201.731γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description