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- EMDB-45423: Yersinia entomophaga toxin complex TcA subunit -

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Basic information

Entry
Database: EMDB / ID: EMD-45423
TitleYersinia entomophaga toxin complex TcA subunit
Map data
Sample
  • Complex: Yersinia entomophaga holotoxin complex in pore conformation
KeywordsToxin / pore-forming / insecticidal / chitinases
Biological speciesYersinia entomophaga (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsLow YS / Landsberg MJ
Funding support Australia, 2 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP220101681 Australia
Australian Research Council (ARC)DP170104484 Australia
CitationJournal: Nat Commun / Year: 2025
Title: Complete structures of the YenTc holotoxin prepore and pore reveal the evolutionary basis for chitinase incorporation into ABC toxins.
Authors: Yu Shang Low / Solace G Roche / Nadezhda A Aleksandrova / Gabriel Foley / Jason Kk Low / Joseph K Box / Tristan I Croll / Irene R Chassagnon / J Shaun Lott / Evelyne Deplazes / Mikael Bodén ...Authors: Yu Shang Low / Solace G Roche / Nadezhda A Aleksandrova / Gabriel Foley / Jason Kk Low / Joseph K Box / Tristan I Croll / Irene R Chassagnon / J Shaun Lott / Evelyne Deplazes / Mikael Bodén / Mark Rh Hurst / Sarah J Piper / Michael J Landsberg /
Abstract: ABC toxins are toxin-translocating, pore-forming proteins found in a wide range of insecticidal bacteria and some mammalian pathogens. The Yersinia entomopahaga toxin complex (YenTc) belongs to a ...ABC toxins are toxin-translocating, pore-forming proteins found in a wide range of insecticidal bacteria and some mammalian pathogens. The Yersinia entomopahaga toxin complex (YenTc) belongs to a distinct subclass of ABC toxins, defined by a divergent molecular architecture. Structural details that define their mechanism of action remain to be elucidated. Here we determine structures of the YenTc holotoxin assembly in both prepore and pore-forming configurations using cryo-EM in conjunction with Alphafold2-assisted structural modelling of flexible domains. We define the structural mechanism via which enzymatically-active chitinase subunits are incorporated, and show using phylogenetic analyses that this subclass-defining feature has evolved relatively recently. Our structures point to the existence of distinct conformational states in YenTc, which may distinguish it from other structurally-characterised ABC toxins, or represent states on a shared mechanistic trajectory. Thus, our findings enhance our understanding of the structural diversity that defines distinct ABC toxin subclasses.
History
DepositionJun 19, 2024-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45423.png

Downloads & links

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Map

FileDownload / File: emd_45423.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
2.9 Å/pix.
x 256 pix.
= 743.04 Å		2.9 Å/pix.
x 256 pix.
= 743.04 Å		2.9 Å/pix.
x 256 pix.
= 743.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.9025 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.8409159 - 4.0888724
Average (Standard dev.)-0.00163379 (±0.13939837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 743.04004 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45423_msk_1.map
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Half map: #2

Fileemd_45423_half_map_1.map
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Half map: #1

Fileemd_45423_half_map_2.map
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Sample components

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Entire : Yersinia entomophaga holotoxin complex in pore conformation

EntireName: Yersinia entomophaga holotoxin complex in pore conformation
Components
  • Complex: Yersinia entomophaga holotoxin complex in pore conformation

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Supramolecule #1: Yersinia entomophaga holotoxin complex in pore conformation

SupramoleculeName: Yersinia entomophaga holotoxin complex in pore conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Yersinia entomophaga (bacteria)
Molecular weightTheoretical: 2.5 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ogd

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 23515
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

6ogd


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL

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