3RKO | pdb_00003rko

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 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/nature10330
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 450.86 kDa 
  • Atom Count: 30,310 
  • Modeled Residue Count: 3,904 
  • Deposited Residue Count: 4,076 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT LA [auth L],
G [auth B]
613Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT MB [auth M],
H [auth C]
509Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT NC [auth N],
I [auth D]
485Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT KD [auth K],
J [auth G]
100Escherichia coli BL21(DE3)Mutation(s): 0 
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))
Explore C5W716 
Go to UniProtKB:  C5W716
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5W716
Sequence Annotations
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT AE [auth A],
K [auth E]
147Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT JF [auth J],
L [auth F]
184Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 1.6.5.3

Small Molecules

Ligands 2 Unique
IDChains Name / 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
LFA

Query on LFA



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth D]
EA [auth D]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.282 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
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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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description