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: nuoLECBD_1383HO396_11190
EC: 1.6.5.3
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I membrane domain
Find proteins for A0A140N7P6 (Escherichia coli (strain B / BL21-DE3))
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  • Reference Sequence
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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: nuoMECBD_1384HO396_11185
EC: 1.6.5.3
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I membrane domain
Find proteins for A0A140N571 (Escherichia coli (strain B / BL21-DE3))
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  • Reference Sequence
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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: nuoNECBD_1385HO396_11180
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I membrane domain
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: nuoKB21_02164ECBD_1382ECD_02204
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I membrane domain
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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: nuoAECBD_1373HO396_11240
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I membrane domain
Find proteins for A0A140N7N4 (Escherichia coli (strain B / BL21-DE3))
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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: nuoJECBD_1381HO396_11200
EC: 1.6.5.3 (PDB Primary Data), 7.1.1 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex I
Protein: 
Complex I membrane domain
Find proteins for A0A140N7W8 (Escherichia coli (strain B / BL21-DE3))
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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