6SUE

Structure of Photorhabdus luminescens Tc holotoxin pore, Mutation TccC3-D651A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a Tc holotoxin pore provides insights into the translocation mechanism.

Roderer, D.Hofnagel, O.Benz, R.Raunser, S.

(2019) Proc Natl Acad Sci U S A 116: 23083-23090

  • DOI: 10.1073/pnas.1909821116
  • Primary Citation of Related Structures:  
    6SUE, 6SUF

  • PubMed Abstract: 
  • Tc toxins are modular toxin systems of insect and human pathogenic bacteria. They are composed of a 1.4-MDa pentameric membrane translocator (TcA) and a 250-kDa cocoon (TcB and TcC) encapsulating the 30-kDa toxic enzyme (C terminus of TcC). Binding o ...

    Tc toxins are modular toxin systems of insect and human pathogenic bacteria. They are composed of a 1.4-MDa pentameric membrane translocator (TcA) and a 250-kDa cocoon (TcB and TcC) encapsulating the 30-kDa toxic enzyme (C terminus of TcC). Binding of Tc toxins to target cells and a pH shift trigger the conformational transition from the soluble prepore state to the membrane-embedded pore. Subsequently, the toxic enzyme is translocated and released into the cytoplasm. A high-resolution structure of a holotoxin embedded in membranes is missing, leaving open the question of whether TcB-TcC has an influence on the conformational transition of TcA. Here we show in atomic detail a fully assembled 1.7-MDa Tc holotoxin complex from Photorhabdus luminescens in the membrane. We find that the 5 TcA protomers conformationally adapt to fit around the cocoon during the prepore-to-pore transition. The architecture of the Tc toxin complex allows TcB-TcC to bind to an already membrane-embedded TcA pore to form a holotoxin. Importantly, assembly of the holotoxin at the membrane results in spontaneous translocation of the toxic enzyme, indicating that this process is not driven by a proton gradient or other energy source. Mammalian lipids with zwitterionic head groups are preferred over other lipids for the integration of Tc toxins. In a nontoxic Tc toxin variant, we can visualize part of the translocating toxic enzyme, which transiently interacts with alternating negative charges and hydrophobic stretches of the translocation channel, providing insights into the mechanism of action of Tc toxins.


    Related Citations: 
    • Structure of a Tc holotoxin pore provides insights into the translocation mechanism
      Roderer, D., Hofnagel, O., Benz, R., Raunser, S.
      () Biorxiv --: --

    Organizational Affiliation

    Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany; raunser@mpi-dortmund.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TcdA1ABCDE2516Photorhabdus luminescensMutation(s): 0 
Gene Names: tcdAtcdA1
Find proteins for Q9RN43 (Photorhabdus luminescens)
Explore Q9RN43 
Go to UniProtKB:  Q9RN43
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TcdB2,TccC3F2439Photorhabdus luminescensMutation(s): 1 
Gene Names: tcdB2
Find proteins for Q8GF99 (Photorhabdus luminescens)
Explore Q8GF99 
Go to UniProtKB:  Q8GF99
Find proteins for Q8GF97 (Photorhabdus luminescens)
Explore Q8GF97 
Go to UniProtKB:  Q8GF97
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany615984

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references