8RVG | pdb_00008rvg

Structure of the binding domain of BoNT/A mutant Y1117V in complex with the GD1a ganglioside receptor

• PDB DOI: https://doi.org/10.2210/pdb8RVG/pdb

• Classification: TOXIN
• Organism(s): Clostridium botulinum
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2024-02-01 Released: 2025-02-12 
• Deposition Author(s): Masuyer, G., Stenmark, P.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.260 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Botulinum neurotoxin A mutants with enhanced ganglioside binding show improved potency and altered ganglioside selectivity.

Masuyer, G., Rummel, A., Stenmark, P.

(2025) Commun Chem 8: 171-171

• PubMed: 40467754 
• DOI: https://doi.org/10.1038/s42004-025-01569-0
• Primary Citation Related Structures: 
  8RVG, 8RVH, 8RVI


• PubMed Abstract: 
  

  Botulinum neurotoxins are the causative agents of botulism, a lethal paralytic disease, but are also one of the most commonly used therapeutics for the treatment of numerous neuromuscular conditions. These toxins recognise motor nerve terminals with high specificity and affinity by using a dual binding mechanism involving gangliosides and protein receptors. The initial recognition of gangliosides is crucial for the toxins' potency. In this study, we employed a synaptosome-binding screening strategy to identify BoNT/A mutants with enhanced ganglioside-binding which translated into improved potency. X-ray crystallography and receptor-binding assays were used to elucidate the molecular mechanisms underlying the increased affinity or altered ganglioside selectivity of these mutants. Our findings provide a basis for the development of BoNT/A variants with enhanced therapeutic potential.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden.
Institute of Toxicology, Hannover Medical School, 30623, Hannover, Germany. [e-mail].
Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 104.97 kDa 
• Atom Count: 7,268 
• Modeled Residue Count: 832 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin A heavy chain	A, B	444	Clostridium botulinum	Mutation(s): 1  Gene Names: botA, atx, bonT
UniProt
Find proteins for P0DPI0 (Clostridium botulinum) Explore P0DPI0  Go to UniProtKB:  P0DPI0

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose	C [auth G], D [auth H]	4		N/A
Glycosylation Resources
GlyTouCan: G02162KR GlyCosmos: G02162KR GlyGen: G02162KR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.260 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.531	α = 90
b = 104.421	β = 90
c = 112.889	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Masuyer, G., Stenmark, P.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release
  
• Version 1.1: 2025-08-27
  Changes: Database references