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- PDB-9kyc: PltBd1/PltBd2 heteropentameric holotoxin from E. coli -

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Basic information

Entry
Database: PDB / ID: 9kyc
TitlePltBd1/PltBd2 heteropentameric holotoxin from E. coli
Components
  • (Subtilase cytotoxin subunit B) x 2
  • Cytolethal distending toxin subunit B family protein
  • Pertussis toxin-like subunit ArtA
KeywordsTOXIN / heteropentamer
Function / homology
Function and homology information


catalytic activity / NAD+ poly-ADP-ribosyltransferase activity / extracellular region
Similarity search - Function
Cytolethal distending toxin B / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Enterotoxin / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
Subtilase cytotoxin subunit B / Pertussis toxin-like subunit ArtA / Cytolethal distending toxin subunit B family protein / Subtilase cytotoxin subunit B
Similarity search - Component
Biological speciesSalmonella enterica subsp. diarizonae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsChen, Z. / Wang, D.D. / Gao, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: PLoS Pathog / Year: 2025
Title: Functional synergy of heteropentameric B subunits underlies virulence in a Salmonella A2B5 toxin.
Authors: Dongdong Wang / Zhe Chen / Chunyu Xu / Xuyao Jiao / Min Yue / Xiang Gao /
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 ...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.
History
DepositionDec 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytolethal distending toxin subunit B family protein
B: Pertussis toxin-like subunit ArtA
C: Subtilase cytotoxin subunit B
D: Subtilase cytotoxin subunit B
E: Subtilase cytotoxin subunit B
F: Subtilase cytotoxin subunit B
G: Subtilase cytotoxin subunit B


Theoretical massNumber of molelcules
Total (without water)133,0537
Polymers133,0537
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cytolethal distending toxin subunit B family protein


Mass: 30184.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. diarizonae (bacteria)
Gene: B4V94_22780, CTQ69_05285, DLB95_17835, G0D72_21670, GB480_00980, GBX62_11500
Production host: Escherichia coli (E. coli) / References: UniProt: A0A3V0PQJ3
#2: Protein Pertussis toxin-like subunit ArtA / Pertussis-like toxin subunit ArtA


Mass: 27297.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. diarizonae (bacteria)
Gene: artA, ABB53_009925, B4V94_22795, CNQ75_07295, DLB95_17850, G2916_21300, G2974_22565, G2997_22660, G3A00_19430, GB016_19575, GB034_20690, GB088_22285, GB236_21915, GB246_19590, GB337_19740, ...Gene: artA, ABB53_009925, B4V94_22795, CNQ75_07295, DLB95_17850, G2916_21300, G2974_22565, G2997_22660, G3A00_19430, GB016_19575, GB034_20690, GB088_22285, GB236_21915, GB246_19590, GB337_19740, GB348_18480, GB480_00965, GBS30_22125, GBV97_20145, GBW00_19900, GBX19_22040, GBX62_11515, GBY11_22700, GBY15_15100, GBY49_11210, GBZ04_18540, GBZ10_19960, GBZ12_10540, GBZ37_18520, GBZ41_22405
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I5HFM6
#3: Protein Subtilase cytotoxin subunit B


Mass: 16576.629 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. diarizonae (bacteria)
Gene: DLB95_17855, G0D47_10640, G2916_21295, G2997_22655, G3A00_19435, GB016_19580, GB034_20695, GB088_22290, GB236_21910, GB246_19595, GB337_19745, GB348_18485, GBS30_22120, GBV97_20140, GBW00_ ...Gene: DLB95_17855, G0D47_10640, G2916_21295, G2997_22655, G3A00_19435, GB016_19580, GB034_20695, GB088_22290, GB236_21910, GB246_19595, GB337_19745, GB348_18485, GBS30_22120, GBV97_20140, GBW00_19905, GBX19_22045, GBX62_11520, GBY11_22705, GBY15_15095, GBY49_11215, GBZ10_19965, GBZ12_10545, GBZ37_18525, GBZ41_22400, PG27_18440
Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Z3F2I6
#4: Protein Subtilase cytotoxin subunit B / Subtilase family AB5 toxin binding subunit


Mass: 12920.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. diarizonae (bacteria)
Gene: AH359_15415, B4V94_22805, CNQ75_07285, CTQ69_05310, FNI27_02145, G0D47_10645, G2974_22970, GBZ04_18550, JMJ85_10105, PG27_18445
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I5HFM4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Recombinant Diarizonae toxin (DT) heteropentamer - PltA and PltBd1/Bd2 complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Salmonella enterica subsp. diarizonae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144112 / Symmetry type: POINT
RefinementHighest resolution: 2.94 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048541
ELECTRON MICROSCOPYf_angle_d0.72311624
ELECTRON MICROSCOPYf_dihedral_angle_d4.5521161
ELECTRON MICROSCOPYf_chiral_restr0.0461267
ELECTRON MICROSCOPYf_plane_restr0.0051503

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