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- PDB-9kyd: PltBd1 homopentameric holotoxin from E. coli -

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Basic information

Entry
Database: PDB / ID: 9kyd
TitlePltBd1 homopentameric holotoxin from E. coli
Components
  • Pertussis toxin-like subunit ArtA
  • Subtilase cytotoxin subunit B
KeywordsTOXIN / heteropentamer
Function / homologyBordetella pertussis toxin A / Pertussis toxin, subunit 1 / Enterotoxin / NAD+ poly-ADP-ribosyltransferase activity / extracellular region / 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: 3.05 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

Downloads & links

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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)110,1816
Polymers110,1816
Non-polymers00
Water00
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: 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
#2: Protein
Subtilase cytotoxin subunit B


Mass: 16576.629 Da / Num. of mol.: 5
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
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: Recombinant Diarizonae toxin (DT) homopentamer - PltA and PltBd1 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

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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 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196577 / Symmetry type: POINT
RefinementHighest resolution: 3.05 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036621
ELECTRON MICROSCOPYf_angle_d0.5839016
ELECTRON MICROSCOPYf_dihedral_angle_d5.125899
ELECTRON MICROSCOPYf_chiral_restr0.046965
ELECTRON MICROSCOPYf_plane_restr0.0041167

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