5SV0

Structure of the ExbB/ExbD complex from E. coli at pH 7.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural insight into the role of the Ton complex in energy transduction.

Celia, H.Noinaj, N.Zakharov, S.D.Bordignon, E.Botos, I.Santamaria, M.Barnard, T.J.Cramer, W.A.Lloubes, R.Buchanan, S.K.

(2016) Nature 538: 60-65

  • DOI: 10.1038/nature19757
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In Gram-negative bacteria, outer membrane transporters import nutrients by coupling to an inner membrane protein complex called the Ton complex. The Ton complex consists of TonB, ExbB, and ExbD, and uses the proton motive force at the inner membrane ...

    In Gram-negative bacteria, outer membrane transporters import nutrients by coupling to an inner membrane protein complex called the Ton complex. The Ton complex consists of TonB, ExbB, and ExbD, and uses the proton motive force at the inner membrane to transduce energy to the outer membrane via TonB. Here, we structurally characterize the Ton complex from Escherichia coli using X-ray crystallography, electron microscopy, double electron-electron resonance (DEER) spectroscopy, and crosslinking. Our results reveal a stoichiometry consisting of a pentamer of ExbB, a dimer of ExbD, and at least one TonB. Electrophysiology studies show that the Ton subcomplex forms pH-sensitive cation-selective channels and provide insight into the mechanism by which it may harness the proton motive force to produce energy.


    Organizational Affiliation

    Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255 CNRS/Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, 13402 Marseille Cedex 20, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Biopolymer transport protein ExbB
B, C, D, E, F, G, H, I, J, A
244Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: exbB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
ExbB/ExbD complex associated with TonB complex, pH 7.0
Find proteins for P0ABU7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABU7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
D, F, I
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, I
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 137.166α = 90.00
b = 104.779β = 91.77
c = 149.364γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States1K22AI113078-01
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesZIA DK036139-10
French National Research AgencyFranceANR-14-CE09-0023
Projets internationaux de cooperation scientifiqueFrancePICS05853

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references
  • Version 1.2: 2016-10-19
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-10-04
    Type: Author supporting evidence