3IAS

Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 4 mol/ASU, re-refined to 3.15 angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

Starting Model: experimental
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Literature

Structural basis for the mechanism of respiratory complex I

Berrisford, J.M., Sazanov, L.A.

(2009) J Biol Chem 284: 29773-29783

  • DOI: https://doi.org/10.1074/jbc.M109.032144
  • Primary Citation of Related Structures:  
    3I9V, 3IAM, 3IAS

  • PubMed Abstract: 

    Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source of reactive oxygen species, which may be one of the causes of aging. Dysfunction of complex I is implicated in many human neurodegenerative diseases. We have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 A resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of reactive oxygen species production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide-binding pocket, as well as small but significant shifts of several alpha-helices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby iron-sulfur clusters N2 and N6a/b. Cluster N2 is the electron donor to quinone and is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines.

    • Organizational Affiliation: 

    Medical Research Council Mitochondrial Biology Unit, Cambridge CB20XY, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 1A [auth 1],
I [auth A],
Q [auth J],
Y [auth S]		438Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 2B [auth 2],
J [auth B],
R [auth K],
Z [auth T]		181Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 3AA [auth U],
C [auth 3],
K [auth C],
S [auth L]		783Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 4BA [auth V],
D [auth 4],
L [auth D],
T [auth M]		409Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 5CA [auth W],
E [auth 5],
M [auth E],
U [auth N]		207Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 6DA [auth X],
F [auth 6],
N [auth F],
V [auth O]		181Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 9EA [auth Y],
G [auth 9],
O [auth G],
W [auth P]		182Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 15FA [auth Z],
H [auth 7],
P [auth H],
X [auth Q]		129Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN
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HA [auth 1],
JB [auth J],
VA [auth A],
XB [auth S]		FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4
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AB [auth C]
AC [auth U]
BC [auth U]
CC [auth U]
DB [auth F]
AB [auth C],
AC [auth U],
BC [auth U],
CC [auth U],
DB [auth F],
EB [auth G],
FB [auth G],
FC [auth X],
GA [auth 1],
GC [auth Y],
HC [auth Y],
IB [auth J],
KA [auth 3],
LA [auth 3],
MA [auth 3],
MB [auth L],
NB [auth L],
OB [auth L],
QA [auth 6],
RA [auth 9],
SA [auth 9],
SB [auth O],
TB [auth P],
UA [auth A],
UB [auth P],
WB [auth S],
YA [auth C],
ZA [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
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BB [auth C]
DC [auth U]
IA [auth 2]
KB [auth K]
NA [auth 3]
BB [auth C],
DC [auth U],
IA [auth 2],
KB [auth K],
NA [auth 3],
PB [auth L],
WA [auth B],
YB [auth T]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CA
Query on CA
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CB [auth C]
EC [auth U]
GB [auth G]
HB [auth H]
IC [auth Y]
CB [auth C],
EC [auth U],
GB [auth G],
HB [auth H],
IC [auth Y],
JA [auth 2],
JC [auth Z],
LB [auth K],
OA [auth 3],
PA [auth 3],
QB [auth L],
RB [auth L],
TA [auth 9],
VB [auth P],
XA [auth B],
ZB [auth T]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • 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
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-27
    Changes: Structure summary