Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 150.98 kDa 
• Atom Count: 10851 
• Modelled Residue Count: 1276 
• Deposited Residue Count: 1290 
• Unique protein chains: 1

1S0F

Crystal structure of botulinum neurotoxin type B at pH 7.0

• DOI: 10.2210/pdb1S0F/pdb

• Classification: Toxin, hydrolase
• Organism(s): Clostridium botulinum
• Mutation(s): No 


• Deposited: 2003-12-30 Released: 2004-03-16 
• Deposition Author(s): Eswaramoorthy, S., Kumaran, D., Keller, J., Swaminathan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Literature

Role of metals in the biological activity of Clostridium botulinum neurotoxins

Eswaramoorthy, S., Kumaran, D., Keller, J., Swaminathan, S.

(2004) Biochemistry 43: 2209-2216

• PubMed: 14979717 
• DOI: 10.1021/bi035844k
• Primary Citation of Related Structures:  
  1S0E, 1S0D, 1S0C, 1S0B, 1S0G, 1S0F


• PubMed Abstract: 
  

Clostridium botulinum neurotoxins are the most potent toxins to humans and cause paralysis by blocking neurotransmitter release at the presynaptic nerve terminals. The toxicity involves four steps, viz., binding to neuronal cells, internalization, translocation, and catalytic activity. While the catalytic activity is a zinc endopeptidase activity on the SNARE complex proteins, the translocation is believed to be a pH-dependent process allowing the translocation domain to change its conformation to penetrate the endosomal membrane. Here, we report the crystal structures of botulinum neurotoxin type B at various pHs and of an apo form of the neurotoxin, and discuss the role of metal ions and the effect of pH variation in the biological activity. Except for the perturbation of a few side chains, the conformation of the catalytic domain is unchanged in the zinc-depleted apotoxin, suggesting that zinc's role is catalytic. We have also identified two calcium ions in the molecule and present biochemical evidence to show that they play a role in the translocation of the light chain through the membrane.

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Organizational Affiliation: 

Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin type B	A	1290	Clostridium botulinum	Mutation(s): 0  Gene Names: botB EC: 3.4.24.69
Find proteins for P10844 (Clostridium botulinum) Explore P10844  Go to UniProtKB:  P10844

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.6	α = 90
b = 122.85	β = 112.48
c = 93.41	γ = 90

Software Package:

Software Name	Purpose
MARMAD	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
MARMAD	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-30 
• Released Date: 2004-03-16 
Deposition Author(s): Eswaramoorthy, S., Kumaran, D., Keller, J., Swaminathan, S.

Revision History  

• Version 1.0: 2004-03-16
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance