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- EMDB-62643: PltBd1/PltBd2 heteropentameric holotoxin from S. diarizonae -

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Basic information

Entry
Database: EMDB / ID: EMD-62643
TitlePltBd1/PltBd2 heteropentameric holotoxin from S. diarizonae
Map data
Sample
  • Complex: Diarizonae toxin (DT) heteropentamer - PltA and PltBd1/Bd2 complex
    • Protein or peptide: Pertussis toxin-like subunit ArtA
    • Protein or peptide: Subtilase cytotoxin subunit B
    • Protein or peptide: Subtilase cytotoxin subunit B
  • Ligand: water
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.32 Å
AuthorsChen Z / Wang DD / Gao X
Funding support1 items
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, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62643.png

Downloads & links

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Map

FileDownload / File: emd_62643.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.52 Å/pix.
x 360 pix.
= 187.2 Å		0.52 Å/pix.
x 360 pix.
= 187.2 Å		0.52 Å/pix.
x 360 pix.
= 187.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.0774367 - 2.9432423
Average (Standard dev.)-0.0015921444 (±0.08354515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 187.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62643_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62643_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Diarizonae toxin (DT) heteropentamer - PltA and PltBd1/Bd2 complex

EntireName: Diarizonae toxin (DT) heteropentamer - PltA and PltBd1/Bd2 complex
Components
  • Complex: Diarizonae toxin (DT) heteropentamer - PltA and PltBd1/Bd2 complex
    • Protein or peptide: Pertussis toxin-like subunit ArtA
    • Protein or peptide: Subtilase cytotoxin subunit B
    • Protein or peptide: Subtilase cytotoxin subunit B
  • Ligand: water

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Supramolecule #1: Diarizonae toxin (DT) heteropentamer - PltA and PltBd1/Bd2 complex

SupramoleculeName: Diarizonae toxin (DT) heteropentamer - PltA and PltBd1/Bd2 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Salmonella enterica subsp. diarizonae (bacteria)

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Macromolecule #1: Pertussis toxin-like subunit ArtA

MacromoleculeName: Pertussis toxin-like subunit ArtA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. diarizonae (bacteria)
Molecular weightTheoretical: 25.247219 KDa
SequenceString: IDFVYRVDPN PPDVIFRDGF SLLGYNRDLQ QLISGRSCAG GSSDSRYIVT TSDINKTYAI ARAYYSHSKF KGNLYRYKIR ADNNFYSLT PSVNYLESQG GHFNAYEKSM IRLQSEYVST LSILPENIQK AVALVYDSST GQIKDGTSTI NTDYVSISSV S NPGVIPFL ...String:
IDFVYRVDPN PPDVIFRDGF SLLGYNRDLQ QLISGRSCAG GSSDSRYIVT TSDINKTYAI ARAYYSHSKF KGNLYRYKIR ADNNFYSLT PSVNYLESQG GHFNAYEKSM IRLQSEYVST LSILPENIQK AVALVYDSST GQIKDGTSTI NTDYVSISSV S NPGVIPFL PEPQANTQQR IDAFGSLISS CFSIYSVCQT HRGQKTEVYK MPFYDARPVI QFIISGN

UniProtKB: Pertussis toxin-like subunit ArtA

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Macromolecule #2: Subtilase cytotoxin subunit B

MacromoleculeName: Subtilase cytotoxin subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. diarizonae (bacteria)
Molecular weightTheoretical: 13.201585 KDa
SequenceString:
EWTGDYENIG YFSHEVISEF HVGQIDGGAY FCIKAVKADG SRSTPLIACS VSNESVWAPS FKVLLEQARY FYVTEQSVRI YYDHNVWTN QPFVNTFSTN ALVGLSSCSA ATDCFGPGKP

UniProtKB: Subtilase cytotoxin subunit B

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Macromolecule #3: Subtilase cytotoxin subunit B

MacromoleculeName: Subtilase cytotoxin subunit B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. diarizonae (bacteria)
Molecular weightTheoretical: 12.823359 KDa
SequenceString:
EWTGDSSINY YSDEVISDFH VGQFNRSAYF CIKTVKKSGE GTPIIACALS HDSKWIPSFN IMLEQARNFY ITGHSIRVYV QPNVWSNKS FIEALSSNAL VGLSSCSTSE CFGPVK

UniProtKB: Subtilase cytotoxin subunit B

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 137 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1341334
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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