3M9S

Crystal structure of respiratory complex I from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The architecture of respiratory complex I

Efremov, R.G.Baradaran, R.Sazanov, L.A.

(2010) Nature 465: 441-445

  • DOI: 10.1038/nature09066
  • Primary Citation of Related Structures:  
    3M9S, 3M9C

  • PubMed Abstract: 
  • Complex I is the first enzyme of the respiratory chain and has a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation by an unknown mechanism. Dysfunction of complex I has been implicated in many human neurodegenerative diseases ...

    Complex I is the first enzyme of the respiratory chain and has a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation by an unknown mechanism. Dysfunction of complex I has been implicated in many human neurodegenerative diseases. We have determined the structure of its hydrophilic domain previously. Here, we report the alpha-helical structure of the membrane domain of complex I from Escherichia coli at 3.9 A resolution. The antiporter-like subunits NuoL/M/N each contain 14 conserved transmembrane (TM) helices. Two of them are discontinuous, as in some transporters. Unexpectedly, subunit NuoL also contains a 110-A long amphipathic alpha-helix, spanning almost the entire length of the domain. Furthermore, we have determined the structure of the entire complex I from Thermus thermophilus at 4.5 A resolution. The L-shaped assembly consists of the alpha-helical model for the membrane domain, with 63 TM helices, and the known structure of the hydrophilic domain. The architecture of the complex provides strong clues about the coupling mechanism: the conformational changes at the interface of the two main domains may drive the long amphipathic alpha-helix of NuoL in a piston-like motion, tilting nearby discontinuous TM helices, resulting in proton translocation.


    Organizational Affiliation

    Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 1A [auth 1], N [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))
Explore Q56222 
Go to UniProtKB:  Q56222
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 2B [auth 2], O [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
Find proteins for Q56221 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q56221 
Go to UniProtKB:  Q56221
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 3C [auth 3], P [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
Find proteins for Q56223 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q56223 
Go to UniProtKB:  Q56223
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 4D [auth 4], Q [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
Find proteins for Q56220 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q56220 
Go to UniProtKB:  Q56220
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit CE [auth 5], R [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
Find proteins for Q56219 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q56219 
Go to UniProtKB:  Q56219
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit BF [auth 6], S [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))
Explore Q56218 
Go to UniProtKB:  Q56218
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit IG [auth 9], T [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))
Explore Q56224 
Go to UniProtKB:  Q56224
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 15H [auth 7], U [auth J]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))
Explore Q5SKZ7 
Go to UniProtKB:  Q5SKZ7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 12I [auth L], V [auth O]469Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 13J [auth M], W [auth P]392Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 14K [auth N], X [auth Q]379Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunits 7, 10 and 11L [auth R], Y [auth S]274Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit 8M [auth H], Z [auth T]181Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • 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 
BA [auth 1], LA [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth 1] , DA [auth 3] , EA [auth 3] , FA [auth 3] , HA [auth 6] , IA [auth 9] , JA [auth 9] , KA [auth A] , 
AA [auth 1],  DA [auth 3],  EA [auth 3],  FA [auth 3],  HA [auth 6],  IA [auth 9],  JA [auth 9],  KA [auth A],  NA [auth C],  OA [auth C],  PA [auth C],  RA [auth F],  SA [auth G],  TA [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
CA [auth 2], GA [auth 3], MA [auth B], QA [auth C]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.39α = 90
b = 336.09β = 100.59
c = 262.24γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance