1F82 | pdb_00001f82

BOTULINUM NEUROTOXIN TYPE B CATALYTIC DOMAIN

• PDB DOI: https://doi.org/10.2210/pdb1F82/pdb

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


• Deposited: 2000-06-28 Released: 2000-08-16 
• Deposition Author(s): Hanson, M.A., Stevens, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.276 (Depositor) 
• R-Value Work: 
  0.244 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Cocrystal structure of synaptobrevin-II bound to botulinum neurotoxin type B at 2.0 A resolution.

Hanson, M.A., Stevens, R.C.

(2000) Nat Struct Biol 7: 687-692

• PubMed: 10932255 
• DOI: https://doi.org/10.1038/77997
• Primary Citation Related Structures: 
  1F82


• PubMed Abstract: 
  

  Botulinum neurotoxin serotype B is a zinc protease that disrupts neurotransmitter release by cleaving synaptobrevin-II (Sb2), one of three SNARE proteins involved in neuronal synaptic vesicle fusion. The three-dimensional crystal structure of the apo botulinum neurotoxin serotype B catalytic domain (BoNT/B-LC) has been determined to 2.2 A resolution, and the complex of cleaved Sb2 with the catalytic domain (Sb2-BoNT/B-LC) has been determined to 2.0 A resolution. A comparison of the holotoxin catalytic domain and the isolated BoNT/B-LC structure shows a rearrangement of three active site loops. This rearrangement exposes the BoNT/B active site. The Sb2-BoNT/B-LC structure illustrates two distinct binding regions, which explains the specificity of each botulinum neurotoxin for its synaptic vesicle protein. This observation provides an explanation for the proposed cooperativity between binding of full-length substrate and catalysis and suggest a mechanism of synaptobrevin proteolysis employed by the clostridial neurotoxins.

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Organizational Affiliation: 
• Department of Chemistry and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.08 kDa 
• Atom Count: 3,694 
• Modeled Residue Count: 424 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BOTULINUM NEUROTOXIN TYPE B	A	424	Clostridium botulinum	Mutation(s): 0  EC: 3.4.24.69
UniProt
Find proteins for P10844 (Clostridium botulinum) Explore P10844  Go to UniProtKB:  P10844

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.276 (Depositor) 
• R-Value Work:  0.244 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.807	α = 90
b = 62.684	β = 90
c = 130.278	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-08-16 
Deposition Author(s): Hanson, M.A., Stevens, R.C.

Revision History  

• Version 1.0: 2000-08-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations