5SV0 | pdb_00005sv0

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

• PDB DOI: https://doi.org/10.2210/pdb5SV0/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli DH1
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2016-08-04 Released: 2016-09-28 
• Deposition Author(s): Celia, H., Botos, I., Lloubes, R., Buchanan, S.K., Noinaj, N.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), French National Research Agency, Projets internationaux de cooperation scientifique

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.258 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

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

• PubMed: 27654919 
• DOI: https://doi.org/10.1038/nature19757
• Primary Citation Related Structures: 
  5SV0, 5SV1


• 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 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.

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Organizational Affiliation: 
• Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255 CNRS/Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, 13402 Marseille Cedex 20, France.
National Institute of Diabetes &Digestive &Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
Markey Center for Structural Biology, Department of Biological Sciences, and the Purdue Institute for Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, Indiana 47907, USA.
Fachbereich Physik, Freie Universität, 14195 Berlin, Germany.
Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, 45810 Bochum, Germany.
Departamento de Cirugia Experimental, Instituto de Investigacion Hospital La Paz (IdiPAZ), Paseo de la Castellana 261, 28046 Madrid, Spain.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 264.19 kDa 
• Atom Count: 16,861 
• Modeled Residue Count: 2,225 
• Deposited Residue Count: 2,440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biopolymer transport protein ExbB	A [auth B], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth A]	244	Escherichia coli DH1	Mutation(s): 0  Gene Names: exbB Membrane Entity: Yes
UniProt
Find proteins for P0ABU7 (Escherichia coli (strain K12)) Explore P0ABU7  Go to UniProtKB:  P0ABU7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	K [auth D], L [auth F], N [auth I]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
CA	M [auth I], O [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A [auth B], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth A]	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.258 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.166	α = 90
b = 104.779	β = 91.77
c = 149.364	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Celia, H., Botos, I., Lloubes, R., Buchanan, S.K., Noinaj, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1K22AI113078-01
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	ZIA DK036139-10
French National Research Agency	France	ANR-14-CE09-0023
Projets internationaux de cooperation scientifique	France	PICS05853

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2016-10-05
  Changes: Database references
• Version 1.2: 2016-10-19
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2017-10-04
  Changes: Author supporting evidence
• Version 1.5: 2019-12-11
  Changes: Author supporting evidence
• Version 1.6: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Structure summary