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- PDB-9cbc: Yersinia entomophaga holotoxin complex in pore conformation -

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Basic information

Entry
Database: PDB / ID: 9cbc
TitleYersinia entomophaga holotoxin complex in pore conformation
Components
  • Chitinase 2
  • Toxin subunit YenA1
  • Toxin subunit YenA2
  • Toxin subunit YenB
  • Toxin subunit YenC2
KeywordsTOXIN / pore-forming / insecticidal / chitinases
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region / cytoplasm
Similarity search - Function
YwqJ-like deaminase / YwqJ-like deaminase / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat ...YwqJ-like deaminase / YwqJ-like deaminase / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / ABC toxin, N-terminal domain / ABC toxin N-terminal region / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein / Tc toxin complex TcA C-terminal TcB-binding domain / Neuraminidase-like domain / Regulator of chromosome condensation (RCC1) signature 2. / Rhs repeat-associated core / : / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Integrin alpha, N-terminal / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Toxin subunit YenA1 / Toxin subunit YenA2 / Chitinase 2 / Toxin subunit YenB / Toxin subunit YenC2
Similarity search - Component
Biological speciesYersinia entomophaga (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.43 Å
AuthorsLow, Y.S. / Landsberg, M.J.
Funding support Australia, 2items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin subunit YenA1
B: Toxin subunit YenA2
C: Chitinase 2
D: Toxin subunit YenA1
E: Toxin subunit YenA2
F: Chitinase 2
G: Toxin subunit YenA1
H: Toxin subunit YenA2
I: Chitinase 2
J: Toxin subunit YenA1
K: Toxin subunit YenA2
L: Chitinase 2
M: Toxin subunit YenA1
N: Toxin subunit YenA2
O: Chitinase 2
P: Toxin subunit YenB
Q: Toxin subunit YenC2


Theoretical massNumber of molelcules
Total (without water)2,054,60117
Polymers2,054,60117
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Toxin subunit YenA1


Mass: 129912.320 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A877
#2: Protein
Toxin subunit YenA2


Mass: 156324.938 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A878
#3: Protein
Chitinase 2


Mass: 69740.609 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A879, chitinase
#4: Protein Toxin subunit YenB


Mass: 167147.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A880
#5: Protein Toxin subunit YenC2


Mass: 107563.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A882
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Yersinia entomophaga holotoxin complex in pore conformation
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Yersinia entomophaga (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7Coot0.8.9.3model fitting
8ISOLDE1.6.0model fitting
10PHENIX1.19model refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23515 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 6OGD

6ogd


Accession code: 6OGD / Source name: PDB / Type: experimental model

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