9R8G | pdb_00009r8g

Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the antibacterial function of the Pseudomonas putida effector Tke5.

Velazquez, C.Zabala-Zearreta, M.Paredes, C.Civantos, C.Altuna-Alvarez, J.Bernal, P.Albesa-Jove, D.

(2026) EMBO J 

  • DOI: https://doi.org/10.1038/s44318-025-00689-6
  • Primary Citation of Related Structures:  
    9R8G

  • PubMed Abstract: 

    Pseudomonas putida is a plant-beneficial rhizobacterium that encodes multiple type-VI secretion systems (T6SS) to outcompete phytopathogens in the rhizosphere. Among its antibacterial effectors, Tke5 (a member of the BTH_I2691 protein family) is a potent pore-forming toxin that disrupts ion homeostasis without causing considerable membrane damage. Tke5 harbours an N-terminal MIX domain, which is required for T6SS-dependent secretion in other systems. Many MIX domain-containing effectors require T6SS adaptor proteins (Tap) for secretion, but their molecular mechanisms of adaptor-effector binding remain elusive. Here, we report the 2.8 Å cryo-EM structure of the Tap3-Tke5 complex of P. putida strain KT2440, providing structural and functional insights into how effector Tke5 is recruited by its cognate adaptor protein Tap3. Functional dissection shows that the α-helical region of Tke5 is sufficient to kill intoxicated bacteria, while its β-rich region likely contributes to target membrane specificity. These findings delineate a mechanism of BTH_I2691 proteins for Tap recruitment and toxin activity, contributing to our understanding of a widespread yet understudied toxin family.


  • Organizational Affiliation
    • Instituto Biofisika (CSIC, UPV/EHU), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Leioa, 48940, Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin VasX N-terminal region domain-containing protein996Pseudomonas putida KT2440Mutation(s): 0 
Gene Names: PP_2612
UniProt
Find proteins for Q88JN7 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88JN7 
Go to UniProtKB:  Q88JN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88JN7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4123 domain-containing protein318Pseudomonas putida KT2440Mutation(s): 0 
Gene Names: PP_2613
UniProt
Find proteins for Q88JN6 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88JN6 
Go to UniProtKB:  Q88JN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88JN6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2021-127816NB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Data collection, Database references