3IAM

Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, reduced, 2 mol/ASU, with bound NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

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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: 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 ...

    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.


    Related Citations: 
    • Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus
      Sazanov, L.A., Hinchliffe, P.
      (2006) Science 311: 1430

    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 1A [auth 1], I [auth A]438Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo1TTHA0089
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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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 2B [auth 2], J [auth B]181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo2TTHA0088
EC: 1.6.99.5 (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], K [auth C]783Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo3TTHA0090
EC: 1.6.99.5 (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], L [auth D]409Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo4TTHA0087
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 subunit 5E [auth 5], M [auth E]207Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo5TTHA0086
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 subunit 6F [auth 6], N [auth F]181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo6TTHA0085
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q56218 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 9G [auth 9], O [auth G]182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo9TTHA0092
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q56224 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 15H [auth 7], P [auth H]129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: nqo15TTHA0496
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q5SKZ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
KA [auth A], S [auth 1]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

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JA [auth A], R [auth 1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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EA [auth 6] , FA [auth 9] , GA [auth 9] , IA [auth A] , NA [auth C] , OA [auth C] , PA [auth C] , Q [auth 1] , 
EA [auth 6], FA [auth 9], GA [auth 9], IA [auth A], NA [auth C], OA [auth C], PA [auth C], Q [auth 1], UA [auth F], VA [auth G], W [auth 3], WA [auth G], X [auth 3], Y [auth 3]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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MA [auth B], QA [auth C], U [auth 2], Z [auth 3]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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HA [auth 7], XA [auth H]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA [auth 3] , BA [auth 3] , CA [auth 4] , DA [auth 5] , LA [auth A] , RA [auth C] , SA [auth C] , T [auth 1] , 
AA [auth 3], BA [auth 3], CA [auth 4], DA [auth 5], LA [auth A], RA [auth C], SA [auth C], T [auth 1], TA [auth E], V [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.002α = 90
b = 151.015β = 93.07
c = 216.624γ = 90
Software Package:
Software NamePurpose
SCALAdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment  



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