[English] 日本語
Yorodumi
- EMDB-62646: PltBd2 homopentameric holotoxin from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62646
TitlePltBd2 homopentameric holotoxin from E. coli
Map data
Sample
  • Complex: Recombinant Diarizonae toxin (DT) homopentamer - PltA and PltBd2 complex
    • Protein or peptide: Pertussis toxin-like subunit ArtA
    • Protein or peptide: Subtilase cytotoxin subunit B
Keywordstoxin / heteropentamer
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
Function and homology information
Biological speciesSalmonella enterica subsp. diarizonae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 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

-
Structure visualization

Supplemental images

emd_62646.png

Downloads & links

-
Map

FileDownload / File: emd_62646.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 180 pix.
= 187.2 Å		1.04 Å/pix.
x 180 pix.
= 187.2 Å		1.04 Å/pix.
x 180 pix.
= 187.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-2.7879584 - 5.0560474
Average (Standard dev.)-0.0040722303 (±0.15467133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 187.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_62646_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62646_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Recombinant Diarizonae toxin (DT) homopentamer - PltA and PltBd2 ...

EntireName: Recombinant Diarizonae toxin (DT) homopentamer - PltA and PltBd2 complex
Components
  • Complex: Recombinant Diarizonae toxin (DT) homopentamer - PltA and PltBd2 complex
    • Protein or peptide: Pertussis toxin-like subunit ArtA
    • Protein or peptide: Subtilase cytotoxin subunit B

-
Supramolecule #1: Recombinant Diarizonae toxin (DT) homopentamer - PltA and PltBd2 ...

SupramoleculeName: Recombinant Diarizonae toxin (DT) homopentamer - PltA and PltBd2 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. diarizonae (bacteria)

-
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: 27.29782 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKLILLTLI IASFDIYAID FVYRVDPNPP DVIFRDGFSL LGYNRDLQQL ISGRSCAGGS SDSRYIVTTS DINKTYAIAR AYYSHSKFK GNLYRYKIRA DNNFYSLTPS VNYLESQGGH FNAYEKSMIR LQSEYVSTLS ILPENIQKAV ALVYDSSTGQ I KDGTSTIN ...String:
MKKLILLTLI IASFDIYAID FVYRVDPNPP DVIFRDGFSL LGYNRDLQQL ISGRSCAGGS SDSRYIVTTS DINKTYAIAR AYYSHSKFK GNLYRYKIRA DNNFYSLTPS VNYLESQGGH FNAYEKSMIR LQSEYVSTLS ILPENIQKAV ALVYDSSTGQ I KDGTSTIN TDYVSISSVS NPGVIPFLPE PQANTQQRID AFGSLISSCF SIYSVCQTHR GQKTEVYKMP FYDARPVIQF II SGN

UniProtKB: Pertussis toxin-like subunit ArtA

-
Macromolecule #2: Subtilase cytotoxin subunit B

MacromoleculeName: Subtilase cytotoxin subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. diarizonae (bacteria)
Molecular weightTheoretical: 12.920474 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EWTGDSSINY YSDEVISDFH VGQFNRSAYF CIKTVKKSGE GTPIIACALS HDSKWIPSFN IMLEQARNFY ITGHSIRVYV QPNVWSNKS FIEALSSNAL VGLSSCSTSE CFGPVKP

UniProtKB: Subtilase cytotoxin subunit B

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102088
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more