3RKO

Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

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This is version 1.1 of the entry. See complete history. 


Literature

Structure of the membrane domain of respiratory complex I.

Efremov, R.G., Sazanov, L.A.

(2011) Nature 476: 414-420

  • DOI: 10.1038/nature10330
  • Primary Citation of Related Structures:  
    3RKO

  • PubMed Abstract: 

    • Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases ...

    Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Å resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements.

    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 LG [auth B], A [auth L]613Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoL, ECBD_1383, HO396_11190
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N7P6 (Escherichia coli (strain B / BL21-DE3))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT MH [auth C], B [auth M]509Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoM, ECBD_1384, HO396_11185
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N571 (Escherichia coli (strain B / BL21-DE3))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT NI [auth D], C [auth N]485Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoN, ECBD_1385, HO396_11180
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0A140N755 (Escherichia coli (strain B / BL21-DE3))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT KJ [auth G], D [auth K]100Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoK, B21_02164, ECBD_1382, ECD_02204
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for C5W716 (Escherichia coli (strain B / BL21-DE3))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT AE [auth A], K [auth E]147Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoA, ECBD_1373, HO396_11240
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 JL [auth F], F [auth J]184Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoJ, ECBD_1381, HO396_11200
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA7
Query on CA7
Download Ideal Coordinates CCD File 
 P [auth M], Z [auth C]7-cyclohexylheptyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
C25 H46 O11
BEKAVONQUWHNMM-IYBATYGCSA-N		 Ligand Interaction
LFA
Query on LFA
Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , DA [auth D] , EA [auth D] , FA [auth D] , M [auth L] , N [auth L] , 
AA [auth C],  BA [auth C],  CA [auth C],  DA [auth D],  EA [auth D],  FA [auth D],  M [auth L],  N [auth L],  O [auth L],  Q [auth M],  R [auth M],  S [auth N],  T [auth N],  U [auth N],  V [auth N],  W [auth B],  X [auth B],  Y [auth B]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.98α = 98.51
b = 116.57β = 104.08
c = 191.37γ = 108.51
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2011-11-02
    Changes: Database references