9DDP | pdb_00009ddp

E. coli TonB-ExbBD TonB bound to ExbB chain E

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-08-28 Released: 2025-07-09 
  • Deposition Author(s): Celia, H., Botos, I.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of the E. coli Ton and Tol motor complexes.

Celia, H.Botos, I.Ghirlando, R.Duche, D.Beach, B.M.Lloubes, R.Buchanan, S.K.

(2025) Nat Commun 16: 5506-5506

  • DOI: https://doi.org/10.1038/s41467-025-61286-z
  • Primary Citation of Related Structures:  
    9DDM, 9DDN, 9DDO, 9DDP, 9DDQ

  • PubMed Abstract: 

    The Ton and Tol motor proteins use the proton gradient at the inner membrane of Gram-negative bacteria as an energy source. The generated force is transmitted through the periplasmic space to protein components associated with the outer membrane, either to maintain the outer membrane integrity for the Tol system, or to allow essential nutrients to enter the cell for Ton. We have solved the high-resolution structures of the E. coli TonB-ExbB-ExbD and TolA-TolQ-TolR complexes, revealing the inner membrane embedded engine parts of the Ton and Tol systems, and showing how TonB and TolA interact with the ExbBD and TolQR subcomplexes. Structural similarities between the two motor complexes suggest a common mechanism for the opening of the proton channel and the propagation of the proton motive force into movement of the TonB and TolA subunits. Because TonB and TolA bind at preferential ExbB or TolQ subunits, we propose a new mechanism of assembly of TonB and TolA with their respective ExbBD and TolQR subcomplexes and discuss its impact on the mechanism of action for the Ton and Tol systems.


  • Organizational Affiliation
    • Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Biopolymer transport protein ExbB
A, B, C, D, E
244Escherichia coliMutation(s): 0 
Gene Names: exbBb3006JW2974
UniProt
Find proteins for P0ABU7 (Escherichia coli (strain K12))
Explore P0ABU7 
Go to UniProtKB:  P0ABU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABU7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein TonB261Escherichia coliMutation(s): 0 
Gene Names: tonBexbAb1252JW5195
UniProt
Find proteins for P02929 (Escherichia coli (strain K12))
Explore P02929 
Go to UniProtKB:  P02929
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02929
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Biopolymer transport protein ExbDG [auth Y],
H [auth Z]
163Escherichia coliMutation(s): 0 
Gene Names: exbDb3005JW2973
UniProt
Find proteins for P0ABV2 (Escherichia coli (strain K12))
Explore P0ABV2 
Go to UniProtKB:  P0ABV2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABV2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5084:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesZIA DK011011-17

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references