1F31 | pdb_00001f31

CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH A TRISACCHARIDE

• PDB DOI: https://doi.org/10.2210/pdb1F31/pdb

• Classification: TOXIN
• Organism(s): Clostridium botulinum
• Mutation(s): No 


• Deposited: 2000-05-31 Released: 2000-11-01 
• Deposition Author(s): Swaminathan, S., Eswaramoorthy, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.270 (Depositor) 
• R-Value Work: 
  0.212 (Depositor) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of the catalytic and binding sites of Clostridium botulinum neurotoxin B.

Swaminathan, S., Eswaramoorthy, S.

(2000) Nat Struct Biol 7: 693-699

• PubMed: 10932256 
• DOI: https://doi.org/10.1038/78005
• Primary Citation Related Structures: 
  1EPW, 1F31


• PubMed Abstract: 
  

  Clostridium botulinum neurotoxins are among the most potent toxins to humans. The crystal structures of intact C. botulinum neurotoxin type B (BoNT/B) and its complex with sialyllactose, determined at 1. 8 and 2.6 A resolution, respectively, provide insight into its catalytic and binding sites. The position of the belt region in BoNT/B is different from that in BoNT/A; this observation presents interesting possibilities for designing specific inhibitors that could be used to block the activity of this neurotoxin. The structures of BoNT/B and its complex with sialyllactose provide a detailed description of the active site and a model for interactions between the toxin and its cell surface receptor. The latter may provide valuable information for recombinant vaccine development.

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Organizational Affiliation: 
• Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 151.63 kDa 
• Atom Count: 10,584 
• Modeled Residue Count: 1,280 
• Deposited Residue Count: 1,290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BOTULINUM NEUROTOXIN TYPE B	A	1,290	Clostridium botulinum	Mutation(s): 0  EC: 3.4.24.69
UniProt
Find proteins for P10844 (Clostridium botulinum) Explore P10844  Go to UniProtKB:  P10844

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-alpha-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G13164IZ GlyCosmos: G13164IZ GlyGen: G13164IZ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.270 (Depositor) 
• R-Value Work:  0.212 (Depositor) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.3	α = 90
b = 123.65	β = 113.38
c = 95.56	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-01 
Deposition Author(s): Swaminathan, S., Eswaramoorthy, S.

Revision History  

• Version 1.0: 2000-11-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-09
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary