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 24VA | pdb_000024va

Cryo-EM structure of recombinant Botulinum neurotoxin A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

Recombinant versus native botulinum neurotoxin type A: structural and pharmacodynamic comparison.

Yao, Z., Xu, L., Lu, Y., Gong, H., Sun, X., Zhao, Y., Chen, J., Yang, L., Chen, Q., Yang, W.

(2026) Acta Crystallogr F Struct Biol Commun 82: 391-401

  • DOI: https://doi.org/10.1107/S2053230X26009830
  • Primary Citation Related Structures: 
    24VA

  • PubMed Abstract: 

    Botulinum neurotoxins (BoNTs) are highly potent exotoxins utilized for esthetic and therapeutic indications. Unlike traditional products derived from Clostridium botulinum, this study presents the design, production, structural characterization and preclinical pharmacodynamics of recombinant BoNT type A1 (rBoNT/A, YY001), newly approved by the National Medical Products Administration and the first rBoNT/A product to be licensed for commercialization in the world. Expressed in Escherichia coli and purified to greater than 99% homogeneity, YY001 shares a core amino-acid sequence with BoNT/A1 in Botox. The additional five residues at the N-terminus and six residues at the C-terminus of the light chain (LC), as well as two residues at the N-terminus of the heavy chain (HC), originate from residual amino acids after protease cleavage; mass-spectrometric peptide mapping confirmed this sequence fidelity. Cryo-electron microscopy yields a 3.2 Å resolution map of the full-length active rBoNT/A, revealing a canonical LC-H N -H C three-domain architecture that predominantly adopts an open conformation, with a root-mean-square deviation of 1.3-1.5 Å relative to native BoNT/A. In vivo head-to-head pharmacodynamic studies showed comparable potency between YY001 and Botox in both mouse digit abduction score assay and rat compound muscle action potential assays. Altogether, the structural, biochemical and pharmacological data indicate that YY001 possesses molecular and functional attributes that are highly comparable to those of native BoNT/A, while providing improved manufacturing consistency and reduced biosafety risks.


  • Organizational Affiliation: 
    • Chongqing Claruvis Pharmaceutical Co., Ltd, No. 28 Yuefu Avenue, DaDi (International) Life Science Park, A2, Beibei District, Chongqing 400700, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 149.63 kDa 
  • Atom Count: 10,327 
  • Modeled Residue Count: 1,267 
  • Deposited Residue Count: 1,298 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Botulinum neurotoxin type A448Clostridium botulinum A str. HallMutation(s): 0 
Gene Names: botA, bna, CBO0806, CLC_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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Botulinum neurotoxin A heavy chain850Clostridium botulinum A str. HallMutation(s): 0 
Gene Names: botA, bna, CBO0806, CLC_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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158
RECONSTRUCTIONRELION4

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2026-11-11 
  • Deposition Author(s): Xu, L.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-11-11
    Type: Initial release