9VI0 | pdb_00009vi0

Complex structure of BoNT-like PG1 at pH 6.0

• PDB DOI: https://doi.org/10.2210/pdb9VI0/pdb
• EM Map EMD-65074: EMDB EMDataResource

• Classification: TOXIN
• Organism(s): Paraclostridium ghonii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-17 Released: 2026-10-07 
• Deposition Author(s): Liu, Z., Chen, P.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structure and functional divergence of the non-canonical BoNT-like toxin PG1 and PG2

Yang, J., Liu, Z., Jiang, L., Ye, X., Chao, Y., Ren, J., Zhu, X., Yang, S., Guo, X., Zeng, J., Wu, H., Chen, P., Zhang, S.

(2026) Nat Commun 

• DOI: https://doi.org/10.1038/s41467-026-77991-2

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 142.29 kDa 
• Atom Count: 9,600 
• Modeled Residue Count: 1,196 
• Deposited Residue Count: 1,251 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LC	A	406	Paraclostridium ghonii	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HC	B	845	Paraclostridium ghonii	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-07 
Deposition Author(s): Liu, Z., Chen, P.

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Funding Organization	Location	Grant Number
Other government	China	2024040801020228
Other government	China	2024AFB026

Revision History  

• Version 1.0: 2026-10-07
  Type: Initial release