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

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Open data


ID or keywords:

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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: 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, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62643_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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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