9C4K | pdb_00009c4k

Yersinia entomophaga holotoxin complex in prepore conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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Literature

Complete structures of the YenTc holotoxin prepore and pore reveal the evolutionary basis for chitinase incorporation into ABC toxins.

Low, Y.S.Roche, S.G.Aleksandrova, N.A.Foley, G.Low, J.K.Box, J.K.Croll, T.I.Chassagnon, I.R.Lott, J.S.Deplazes, E.Boden, M.Hurst, M.R.Piper, S.J.Landsberg, M.J.

(2025) Nat Commun 16: 11121-11121

  • DOI: https://doi.org/10.1038/s41467-025-66050-x
  • Primary Citation of Related Structures:  
    9C4K, 9CBC

  • PubMed 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 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.


  • Organizational Affiliation
    • School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin subunit YenA1
A, D, G, J, M
1,164Yersinia entomophagaMutation(s): 0 
UniProt
Find proteins for B6A877 (Yersinia entomophaga)
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Go to UniProtKB:  B6A877
Entity Groups  
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UniProt GroupB6A877
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin subunit YenA2
B, E, H, K, N
1,364Yersinia entomophagaMutation(s): 0 
UniProt
Find proteins for B6A878 (Yersinia entomophaga)
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Go to UniProtKB:  B6A878
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UniProt GroupB6A878
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chitinase 2
C, F, I, L, O
633Yersinia entomophagaMutation(s): 0 
EC: 3.2.1.14
UniProt
Find proteins for B6A879 (Yersinia entomophaga)
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UniProt GroupB6A879
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin subunit YenB1,487Yersinia entomophagaMutation(s): 0 
UniProt
Find proteins for B6A880 (Yersinia entomophaga)
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UniProt GroupB6A880
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin subunit YenC2970Yersinia entomophagaMutation(s): 0 
UniProt
Find proteins for B6A882 (Yersinia entomophaga)
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UniProt GroupB6A882
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP220101681
Australian Research Council (ARC)AustraliaDP170104484

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-31
    Type: Initial release