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 8CPZ | pdb_00008cpz

Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, K1179W mutant


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8CPZ

This is version 1.1 of the entry. See complete history. 

Literature

Multistate kinetics of the syringe-like injection mechanism of Tc toxins.

Ng'ang'a, P.N., Folz, J., Kucher, S., Roderer, D., Xu, Y., Sitsel, O., Belyy, A., Prumbaum, D., Kuhnemuth, R., Assafa, T.E., Dong, M., Seidel, C.A.M., Bordignon, E., Raunser, S.

(2025) Sci Adv 11: eadr2019-eadr2019

  • DOI: https://doi.org/10.1126/sciadv.adr2019
  • Primary Citation Related Structures: 
    8CPZ, 8CQ0, 8CQ2

  • PubMed Abstract: 

    Tc toxins are pore-forming virulence factors of many pathogenic bacteria. Following pH-induced conformational changes, they perforate the target membrane like a syringe to translocate toxic enzymes into a cell. Although this complex transformation has been structurally well studied, the reaction pathway and the resulting temporal evolution have remained elusive. We used an integrated biophysical approach to monitor prepore-to-pore transition and found a reaction time of ~30 hours for a complete transition. We show two asynchronous general steps of the process, shell opening and channel ejection, with the overall reaction pathway being a slow multistep process involving three intermediates. Liposomes, an increasingly high pH, or receptors facilitate shell opening, which is directly correlated with an increased rate of the prepore-to-pore transition. Channel ejection is a near-instantaneous process which occurs with a transition time of <60 milliseconds. Understanding the mechanism of action of Tc toxins and unveiling modulators of the kinetics are key steps toward their application as biomedical devices or biopesticides.


  • Organizational Affiliation: 
    • Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany.

Macromolecule Content 

  • Total Structure Weight: 1,427.16 kDa 
  • Atom Count: 84,420 
  • Modeled Residue Count: 10,610 
  • Deposited Residue Count: 12,675 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TcdA1
A, B, C, D, E
2,535Photorhabdus luminescensMutation(s): 1 
Gene Names: tcdA, tcdA1
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: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Data collection, Database references, Structure summary