3N7J

Crystal structure of botulinum neurotoxin serotype D binding domain

• PDB DOI: https://doi.org/10.2210/pdb3N7J/pdb

• Classification: TOXIN
• Organism(s): Clostridium botulinum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-27 Released: 2010-09-08 
• Deposition Author(s): Fu, Z., Baldwin, M.R., Karalewitz, A., Kroken, A., Barbieri, J.T., Kim, J.-J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.256 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Literature

Identification of a Unique Ganglioside Binding Loop within Botulinum Neurotoxins C and D-SA .

Karalewitz, A.P., Kroken, A.R., Fu, Z., Baldwin, M.R., Kim, J.J., Barbieri, J.T.

(2010) Biochemistry 49: 8117-8126

• PubMed: 20731382 
• DOI: https://doi.org/10.1021/bi100865f
• Primary Citation of Related Structures:  
  3N7J, 3N7K, 3N7L, 3N7M


• PubMed Abstract: 
  

  The botulinum neurotoxins (BoNTs) are the most potent protein toxins for humans. There are seven serotypes of BoNTs (A-G) based on a lack of cross antiserum neutralization. BoNTs utilize gangliosides as components of the host receptors for binding and entry into neurons. Members of BoNT/C and BoNT/D serotypes include mosaic toxins that are organized in D/C and C/D toxins. One D/C mosaic toxin, BoNT/D-South Africa (BoNT/D-SA), was not fully neutralized by immunization with BoNT serotype C or D, which stimulated this study. Here the crystal structures of the receptor binding domains of BoNT/C, BoNT/D, and BoNT/D-SA are presented. Biochemical and cell binding studies show that BoNT/C and BoNT/D-SA possess unique mechanisms for ganglioside binding. These studies provide new information about how the BoNTs can enter host cells as well as a basis for understanding the immunological diversity of these neurotoxins.

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Organizational Affiliation: 

Department of Microbiology and of Molecular Genetics, Medical College of Wisconsin,Milwaukee, Wisconsin 53226-3548, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 48.24 kDa 
• Atom Count: 3,514 
• Modelled Residue Count: 405 
• Deposited Residue Count: 415 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin type D	A	415	Clostridium botulinum	Mutation(s): 0  Gene Names: botD, Clostridium phage d-16 phi
UniProt
Find proteins for P19321 (Clostridium botulinum D phage) Explore P19321  Go to UniProtKB:  P19321

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.256 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.04	α = 90
b = 94.15	β = 90
c = 94.99	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Fu, Z., Baldwin, M.R., Karalewitz, A., Kroken, A., Barbieri, J.T., Kim, J.-J.P.

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2015-01-28
  Changes: Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description