9GY5 | pdb_00009gy5

Crystal structure of the catalytic domain from the BoNT-like toxin complex PG1 of Paeniclostridium ghonii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.250 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.228 (DCC) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9GY5

This is version 1.1 of the entry. See complete history

Literature

Identification and characterization of botulinum neurotoxin-like two-component toxins in Paeniclostridium ghonii.

Lee, P.G.Yin, L.Wei, X.Shi, J.Masuyer, G.Wentz, T.G.Chen, P.Xu, Y.Liang, J.Zhang, H.Persson Kosenina, S.Lobb, B.Mansfield, M.Gill, S.S.Pellett, S.Stenmark, P.Doxey, A.C.Dong, M.

(2025) Sci Adv 11: eadx6145-eadx6145

  • DOI: https://doi.org/10.1126/sciadv.adx6145
  • Primary Citation Related Structures: 
    9GY5

  • PubMed Abstract: 

    Insecticidal bacterial proteins play key roles in insect-bacteria interactions and have been used as biopesticides. Here, we identify two insecticidal proteins in Paeniclostridium ghonii , designated PG-toxin 1 (PG1) and PG-toxin 2 (PG2), which are homologs of botulinum neurotoxins (BoNTs). Unlike BoNTs, PG1 and PG2 contain two separate proteins: One is the protease light chain (LC), and the other is the heavy chain containing the translocation domain and the receptor binding domain. Crystal and cryo-electron microscopy structures show a conserved BoNT-like architecture but without an interchain disulfide bond. Functional characterizations establish that the LCs of PG1 and PG2 cleave insect synaptosomal-associated protein 25 (SNAP25), but not human or rat SNAP25, and microinjection of PG1 and PG2 caused paralysis and death in Drosophila and Aedes mosquitoes. These findings identified unique two-component BoNT-like insecticidal proteins, revealing insights into the evolution of the BoNT family of toxins, and broadening our understanding of bacteria that can be used for biopest controls.


  • Organizational Affiliation
    • Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 45.29 kDa 
  • Atom Count: 3,078 
  • Modeled Residue Count: 362 
  • Deposited Residue Count: 394 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Catalytic domain from the BoNT-like toxin complex PG1 of Paeniclostridium ghonii394Paraclostridium ghoniiMutation(s): 0 
EC: 3.4.24.69

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
G [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.250 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.228 (DCC) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.217α = 90
b = 79.217β = 90
c = 274.532γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2022-03681
CancerfondenSweden20 1287 PjF
Novo Nordisk FoundationDenmarkNNF20OC0064789

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Database references