9CZC | pdb_00009czc

CryoEM structure of BoNT/E-LCHn domain at pH5

  • Classification: TOXIN
  • Organism(s): Clostridium botulinum
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-08-05 Released: 2026-07-22 
  • Deposition Author(s): Gao, L.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9CZC

This is version 1.0 of the entry. See complete history

Literature

A belt-buckle checkpoint regulates the onset of botulinum neurotoxin intoxication.

Chen, B.Gao, L.Bonninger, M.Huang, T.Krez, N.Wen, W.Bowen, M.Lou, J.Marks, J.D.Rummel, A.Jin, R.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-74499-7
  • Primary Citation Related Structures: 
    9CZB, 9CZC, 9NEY

  • PubMed Abstract: 

    Fast-acting botulinum neurotoxins (BoNTs) are highly desirable for both medical and aesthetic indications, but the underlying mechanism for the differing onset of BoNTs' action remains unknown. Here, we demonstrate that the "belt" of BoNTs, a largely unstructured loop wrapping around their catalytic light chain (LC), is key to onset of intoxication. The more flexible BoNT/E belt promotes quicker LC translocation into the neuronal cytosol, leading to faster onset of action compared to BoNT/A. Furthermore, we discover a "belt-buckle" checkpoint that regulates this process. By loosening the BoNT/A belt-buckle via protein engineering, we enhance its sensitivity to acidic pH, leading to an accelerated onset of action. Conversely, locking the belt-buckle with an antibody neutralizes BoNT/A. Our findings open avenues for developing fast-acting BoNTs and effective countermeasures.


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

Macromolecule Content 

  • Total Structure Weight: 94.45 kDa 
  • Atom Count: 6,214 
  • Modeled Residue Count: 796 
  • Deposited Residue Count: 831 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bont/EA [auth B]831Clostridium botulinumMutation(s): 0 
Gene Names: bont/EbontEEXM65_05465FC774_00665FDB51_03615FDG31_05035
UniProt
Find proteins for Q54A79 (Clostridium botulinum)
Explore Q54A79 
Go to UniProtKB:  Q54A79
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54A79
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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: 2026-07-22 
  • 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: 2026-07-22
    Type: Initial release