8CP6 | pdb_00008cp6

Type six secretion system exported effector 5 (Tse5)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Structural and functional insights into the delivery of a bacterial Rhs pore-forming toxin to the membrane.

Gonzalez-Magana, A.Tascon, I.Altuna-Alvarez, J.Queralt-Martin, M.Colautti, J.Velazquez, C.Zabala, M.Rojas-Palomino, J.Cardenas, M.Alcaraz, A.Whitney, J.C.Ubarretxena-Belandia, I.Albesa-Jove, D.

(2023) Nat Commun 14: 7808-7808

  • DOI: https://doi.org/10.1038/s41467-023-43585-5
  • Primary Citation Related Structures: 
    8CP6

  • PubMed Abstract: 

    Bacterial competition is a significant driver of toxin polymorphism, which allows continual compensatory evolution between toxins and the resistance developed to overcome their activity. Bacterial Rearrangement hot spot (Rhs) proteins represent a widespread example of toxin polymorphism. Here, we present the 2.45 Å cryo-electron microscopy structure of Tse5, an Rhs protein central to Pseudomonas aeruginosa type VI secretion system-mediated bacterial competition. This structural insight, coupled with an extensive array of biophysical and genetic investigations, unravels the multifaceted functional mechanisms of Tse5. The data suggest that interfacial Tse5-membrane binding delivers its encapsulated pore-forming toxin fragment to the target bacterial membrane, where it assembles pores that cause cell depolarisation and, ultimately, bacterial death.


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

Macromolecule Content 

  • Total Structure Weight: 149.02 kDa 
  • Atom Count: 8,899 
  • Modeled Residue Count: 1,129 
  • Deposited Residue Count: 1,343 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Toxin protein Tse573Pseudomonas aeruginosaMutation(s): 0 
Gene Names: tse5PA2684
UniProt
Find proteins for Q9I0F4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I0F4 
Go to UniProtKB:  Q9I0F4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I0F4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Toxin protein Tse51,121Pseudomonas aeruginosaMutation(s): 0 
Gene Names: tse5PA2684
UniProt
Find proteins for Q9I0F4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I0F4 
Go to UniProtKB:  Q9I0F4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I0F4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Toxin protein Tse5149Pseudomonas aeruginosaMutation(s): 0 
Gene Names: tse5PA2684
UniProt
Find proteins for Q9I0F4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I0F4 
Go to UniProtKB:  Q9I0F4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I0F4
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentIT1745-22
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2021-127816NB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release