9ARK | pdb_00009ark

CryoEM structure of BoNT-NTNH-OrfX2 complex from Clostridium botulinum E1, minor class


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Botulinum neurotoxins exploit host digestive proteases to boost their oral toxicity via activating OrfXs/P47.

Gao, L.Nowakowska, M.B.Selby, K.Przykopanski, A.Chen, B.Kruger, M.Douillard, F.P.Lam, K.H.Chen, P.Huang, T.Minton, N.P.Dorner, M.B.Dorner, B.G.Rummel, A.Lindstrom, M.Jin, R.

(2025) Nat Struct Mol Biol 32: 864-875

  • DOI: https://doi.org/10.1038/s41594-024-01479-0
  • Primary Citation of Related Structures:  
    9ARJ, 9ARK, 9ARL

  • PubMed Abstract: 

    Botulinum neurotoxins (BoNTs) rank among the most potent toxins and many of them are produced by bacteria carrying the orfX gene cluster that also encodes four nontoxic proteins (OrfX1, OrfX2, OrfX3 and P47). The orfX gene cluster is also found in the genomes of many non-BoNT-producing bacteria, often alongside genes encoding oral insecticidal toxins. However, the functions of these OrfXs and P47 remain elusive. Here, we demonstrate that the combined action of all four components (OrfXs and P47) drastically boosts the oral toxicity of BoNT in mice, following proteolytic activation by digestive proteases that oral toxins regularly confront. In particular, OrfX2 adopts a self-inhibiting state, engaging with BoNT through another clostridial protein, nontoxic non-hemagglutinin (NTNH), only after proteolytic activation. Cryo-electron microscopy studies unveil that two molecules of protease-activated OrfX2 simultaneously associate with NTNH, a binding mode crucial for boosting BoNT oral toxicity. Collectively, these studies offer novel insights into the physiological functions and regulatory mechanisms of OrfXs and P47 of BoNTs, shedding light on the pathogenesis of other bacterial toxins associated with homologous OrfXs and P47.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Botulinum neurotoxin1,252Clostridium botulinum E1 str. 'BoNT E BelugaMutation(s): 3 
Gene Names: bont
UniProt
Find proteins for Q00496 (Clostridium botulinum)
Explore Q00496 
Go to UniProtKB:  Q00496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00496
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidase M271,163Clostridium botulinum E1 str. 'BoNT E BelugaMutation(s): 0 
Gene Names: FDG31_05030
UniProt
Find proteins for P46082 (Clostridium botulinum)
Explore P46082 
Go to UniProtKB:  P46082
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UniProt GroupP46082
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin748Clostridium botulinum E1 str. 'BoNT E BelugaMutation(s): 0 
Gene Names: FDG31_05015
UniProt
Find proteins for C1FUH4 (Clostridium botulinum (strain Kyoto / Type A2))
Explore C1FUH4 
Go to UniProtKB:  C1FUH4
Entity Groups  
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UniProt GroupC1FUH4
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-01-22 
  • Deposition Author(s): Gao, L.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI139087
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI158503
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI163178

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-14
    Changes: Data collection
  • Version 1.3: 2025-05-28
    Changes: Data collection, Database references