5LKH

Cryo-EM structure of the Tc toxin TcdA1 in its pore state (obtained by flexible fitting)


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 1.4 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: 10.1038/nsmb.3281
  • Primary Citation of Related Structures:  

  • 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 electro ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TcdA1
A, B, C, D, E
2516Photorhabdus luminescensMutation(s): 0 
Gene Names: tcdA (tcdA1)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Adventitious Membrane Proteins: Alpha-helical Pore-forming Toxins.
Protein: 
Tc Toxin, TcA prepore (TcdA1) subunit
Find proteins for Q9RN43 (Photorhabdus luminescens)
Go to UniProtKB:  Q9RN43
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-07
    Type: Database references
  • Version 1.2: 2016-10-19
    Type: Database references
  • Version 1.3: 2017-08-02
    Type: Data collection, Experimental preparation
  • Version 1.4: 2019-10-23
    Type: Data collection, Other