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- PDB-9kyb: PltBd1/PltBd2 heteropentameric holotoxin from S. diarizonae -

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Basic information

Entry
Database: PDB / ID: 9kyb
TitlePltBd1/PltBd2 heteropentameric holotoxin from S. diarizonae
Components
  • (Subtilase cytotoxin subunit B) x 2
  • Pertussis toxin-like subunit ArtA
KeywordsTOXIN / heteropentamer / virulence factor
Function / homologyBordetella pertussis toxin A / Pertussis toxin, subunit 1 / Enterotoxin / NAD+ poly-ADP-ribosyltransferase activity / extracellular region / Subtilase cytotoxin subunit B / Pertussis toxin-like subunit ArtA / Subtilase cytotoxin subunit B
Function and homology information
Biological speciesSalmonella enterica subsp. diarizonae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.32 Å
AuthorsChen, Z. / Wang, D.D. / Gao, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Functional Synergy of Heteropentameric B Subunits Underlies Virulence in a Salmonella A2B5 Toxin
Authors: Wang, D. / Chen, Z. / Xu, C. / Jiao, X. / Yue, M. / Gao, X.
History
DepositionDec 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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)90,4996
Polymers90,4996
Non-polymers00
Water2,468137
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 Pertussis toxin-like subunit ArtA / Pertussis-like toxin subunit ArtA


Mass: 25247.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. diarizonae (bacteria)
References: UniProt: A0A2I5HFM6
#2: Protein Subtilase cytotoxin subunit B


Mass: 13201.585 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. diarizonae (bacteria)
References: UniProt: A0A627X696
#3: Protein Subtilase cytotoxin subunit B / Subtilase family AB5 toxin binding subunit


Mass: 12823.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. diarizonae (bacteria)
References: UniProt: A0A2I5HFM4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
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: Diarizonae toxin (DT) heteropentamer - PltA and PltBd1/Bd2 complex
Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Salmonella enterica subsp. diarizonae (bacteria)
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: 60 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: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1341334 / Symmetry type: POINT
RefinementHighest resolution: 2.32 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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