9KYC | pdb_00009kyc

PltBd1/PltBd2 heteropentameric holotoxin from E. coli


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Functional synergy of heteropentameric B subunits underlies virulence in a Salmonella A2B5 toxin.

Wang, D.Chen, Z.Xu, C.Jiao, X.Yue, M.Gao, X.

(2025) PLoS Pathog 21: e1013684-e1013684

  • DOI: https://doi.org/10.1371/journal.ppat.1013684
  • Primary Citation of Related Structures:  
    9KYB, 9KYC, 9KYD, 9KYE

  • PubMed Abstract: 

    AB5-type toxins are critical virulence factors in bacterial pathogenesis. Despite the identification of various B subunits in AB5 toxins across different pathogens, their assembly mechanisms and biological significance remain poorly understood. In this study, we identified and characterized a typhoid toxin-like A2B5 toxin, designated diarizonae toxin (DiaT), as a key virulence factor in Salmonella diarizonae. The DiaT genomic islet encodes two distinct B subunits, PltBd1 and PltBd2, which exhibit unique functional roles. Through genetic and functional analyses, we demonstrate that the heteropentameric assembly of PltBd1 and PltBd2 is essential for cytotoxicity, with our data suggesting PltBd1 facilitates toxin secretion and PltBd2 mediates host cell targeting. Cryo-EM structural analysis of endogenously expressed DiaT reveals a heteropentameric holotoxin with a 3:2 stoichiometry of PltBd1 to PltBd2, potentially stabilized by the PltA subunit. These findings uncover a novel assembly mechanism and synergistic functionality between distinct B subunits, advancing our understanding of the evolutionary diversity and functional complexity of AB5 toxins. This work provides new insights into bacterial pathogenesis and highlights potential targets for therapeutic intervention.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytolethal distending toxin subunit B family protein270Salmonella enterica subsp. diarizonaeMutation(s): 0 
Gene Names: B4V94_22780CTQ69_05285DLB95_17835G0D72_21670GB480_00980GBX62_11500
UniProt
Find proteins for A0A3V0PQJ3 (Salmonella diarizonae)
Explore A0A3V0PQJ3 
Go to UniProtKB:  A0A3V0PQJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3V0PQJ3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis toxin-like subunit ArtA243Salmonella enterica subsp. diarizonaeMutation(s): 0 
Gene Names: 
UniProt
Find proteins for A0A2I5HFM6 (Salmonella diarizonae)
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Go to UniProtKB:  A0A2I5HFM6
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UniProt GroupA0A2I5HFM6
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Subtilase cytotoxin subunit B
C, F, G
150Salmonella enterica subsp. diarizonaeMutation(s): 0 
Gene Names: 
UniProt
Find proteins for A0A3Z3F2I6 (Salmonella diarizonae)
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Go to UniProtKB:  A0A3Z3F2I6
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UniProt GroupA0A3Z3F2I6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Subtilase cytotoxin subunit B
D, E
116Salmonella enterica subsp. diarizonaeMutation(s): 0 
Gene Names: AH359_15415B4V94_22805CNQ75_07285CTQ69_05310FNI27_02145G0D47_10645G2974_22970GBZ04_18550JMJ85_10105PG27_18445
UniProt
Find proteins for A0A2I5HFM4 (Salmonella diarizonae)
Explore A0A2I5HFM4 
Go to UniProtKB:  A0A2I5HFM4
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UniProt GroupA0A2I5HFM4
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Data collection, Database references