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 

wwPDB Validation 3D Report Full Report


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 impl ...

    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 LB, L613Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1383
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 MC, M509Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1384
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 ND, N485Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoN, ECBD_1385
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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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT KG, K100Escherichia 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 protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex I		Protein: 
Complex I membrane domain
Find proteins for C5W716 (Escherichia coli (strain B / BL21-DE3))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT AA, E147Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoA, ECBD_1373
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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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT JF, J184Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1381
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
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C, M
7-cyclohexylheptyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
C25 H46 O11
BEKAVONQUWHNMM-IYBATYGCSA-N		 Ligand Interaction
LFA
Query on LFA
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B, C, D, L, M, N
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 

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