6H6E | pdb_00006h6e

PTC3 holotoxin complex from Photorhabdus luminecens in prepore state (TcdA1, TcdB2, TccC3)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Tc toxin activation requires unfolding and refolding of a beta-propeller.

Gatsogiannis, C.Merino, F.Roderer, D.Balchin, D.Schubert, E.Kuhlee, A.Hayer-Hartl, M.Raunser, S.

(2018) Nature 563: 209-213

  • DOI: https://doi.org/10.1038/s41586-018-0556-6
  • Primary Citation Related Structures: 
    6H6E, 6H6F, 6H6G

  • PubMed Abstract: 

    Tc toxins secrete toxic enzymes into host cells using a unique syringe-like injection mechanism. They are composed of three subunits, TcA, TcB and TcC. TcA forms the translocation channel and the TcB-TcC heterodimer functions as a cocoon that shields the toxic enzyme. Binding of the cocoon to the channel triggers opening of the cocoon and translocation of the toxic enzyme into the channel. Here we show in atomic detail how the assembly of the three components activates the toxin. We find that part of the cocoon completely unfolds and refolds into an alternative conformation upon binding. The presence of the toxic enzyme inside the cocoon is essential for its subnanomolar binding affinity for the TcA subunit. The enzyme passes through a narrow negatively charged constriction site inside the cocoon, probably acting as an extruder that releases the unfolded protein with its C terminus first into the translocation channel.


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

Macromolecule Content 

  • Total Structure Weight: 1,689.83 kDa 
  • Atom Count: 112,922 
  • Modeled Residue Count: 14,231 
  • Deposited Residue Count: 15,014 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TcdB2,TccC32,434Photorhabdus luminescensMutation(s): 0 
Gene Names: tcdB2TccC3
UniProt
Find proteins for Q8GF97 (Photorhabdus luminescens)
Explore Q8GF97 
Go to UniProtKB:  Q8GF97
Find proteins for Q8GF99 (Photorhabdus luminescens)
Explore Q8GF99 
Go to UniProtKB:  Q8GF99
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ8GF97Q8GF99
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPHIRE
MODEL REFINEMENTRosetta
MODEL REFINEMENTNAMD2.12

Structure Validation

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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: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Refinement description