5LKI

Cryo-EM structure of the Tc toxin TcdA1 in its pore state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

Membrane insertion of a Tc toxin in near-atomic detail.

Gatsogiannis, C.Merino, F.Prumbaum, D.Roderer, D.Leidreiter, F.Meusch, D.Raunser, S.

(2016) Nat Struct Mol Biol 23: 884-890

  • DOI: https://doi.org/10.1038/nsmb.3281
  • Primary Citation of Related Structures:  
    5LKH, 5LKI

  • PubMed Abstract: 

    Tc toxins from pathogenic bacteria use a special syringe-like mechanism to perforate the host cell membrane and inject a deadly enzyme into the host cytosol. The molecular mechanism of this unusual injection system is poorly understood. Using electron cryomicroscopy, we determined the structure of TcdA1 from Photorhabdus luminescens embedded in lipid nanodiscs. In our structure, compared with the previous structure of TcdA1 in the prepore state, the transmembrane helices rearrange in the membrane and open the initially closed pore. However, the helices do not span the complete membrane; instead, the loops connecting the helices form the rim of the funnel. Lipid head groups reach into the space between the loops and consequently stabilize the pore conformation. The linker domain is folded and packed into a pocket formed by the other domains of the toxin, thereby considerably contributing to stabilization of the pore state.


  • Organizational Affiliation

    Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TcdA1
A, B, C, D, E
2,516Photorhabdus luminescensMutation(s): 0 
Gene Names: tcdAtcdA1
UniProt
Find proteins for Q9RN43 (Photorhabdus luminescens)
Explore Q9RN43 
Go to UniProtKB:  Q9RN43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RN43
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX
MODEL REFINEMENTREFMAC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany615984
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2016-10-19
    Changes: Database references
  • Version 1.3: 2017-08-02
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2018-10-17
    Changes: Author supporting evidence, Data collection, Refinement description
  • Version 1.5: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.6: 2019-10-23
    Changes: Data collection, Other
  • Version 1.7: 2024-05-15
    Changes: Data collection, Database references