[English] 日本語
Yorodumi
- PDB-9kyc: PltBd1/PltBd2 heteropentameric holotoxin from E. coli -

+
Open data


ID or keywords:

Loading...

-
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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
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