9VCS | pdb_00009vcs

Cryo-EM structure of semi-closed state of Botulinum neurotoxin serotype A at pH 7.4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9VCS

This is version 1.0 of the entry. See complete history

Literature

Cryo-EM Structure Guided Engineering of Botulinum Neurotoxin A With Advanced Receptor Binding Affinity and Therapeutical Benefits.

Wang, W.Zerang, Z.You, L.Liu, Z.Nie, R.Qi, F.Gao, F.Zhao, C.Ma, W.He, J.Wang, X.Wu, S.Liu, B.Liu, X.Lei, D.Zhi, D.Wang, D.

(2026) Adv Sci (Weinh) : e16713-e16713

  • DOI: https://doi.org/10.1002/advs.202516713
  • Primary Citation Related Structures: 
    9GKQ, 9VCS

  • PubMed Abstract: 

    Botulinum neurotoxin type A (BoNT/A) has been extensively used in treating a wide range of neurological disorders and aesthetics. However, insufficient binding affinity between BoNT/A and its receptor SV2C could lead to mild to severe side effects. An open active conformation of BoNT/A cryo-EM structure at a resolution of ∼2.85 Å was resolved. Guided by the BoNT/A cryo-EM structure, saturation mutagenesis libraries were constructed and screened by BACTH system to identify mutants that can boost toxin-SV2C affinity. The engineered toxin binding domain achieved up to approximately six-fold improved affinity in SPR analysis, and the engineered toxins exhibited significantly improved binding capacity, and enhanced SNAP25 cleavage efficacy in cultured neurons. Preclinical animal studies, including MLB, DAS, sweat test, and PET/CT assays, demonstrated that the engineered BoNT/A VLTS has higher potency, lower diffusion, and significantly better safety profiles than the BoNT/A wt, which can reduce side effects and benefit future therapeutic applications.


  • Organizational Affiliation
    • School of Pharmacy, Joint Drug Development and Innovation Centre For Neurological Disorders of Lanzhou University-China National Biotec Group-Lanzhou Biotechnology Development Co., Lanzhou University, Lanzhou, Gansu, P. R. China.

Macromolecule Content 

  • Total Structure Weight: 151.02 kDa 
  • Atom Count: 10,158 
  • Modeled Residue Count: 1,245 
  • Deposited Residue Count: 1,308 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Botulinum neurotoxin type A1,308Clostridium botulinum A str. HallMutation(s): 0 
Gene Names: botAbnaCBO0806CLC_0862
UniProt
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A))
Explore P0DPI1 
Go to UniProtKB:  P0DPI1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DPI1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82073825
National Natural Science Foundation of China (NSFC)China32171300
Other government22ZD6FA053
Other government20JR10RA619
Other governmentlzuyxcx-2022-197

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-22
    Type: Initial release