Crystal structure of botulinum neurotoxin type B at pH 6.0

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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This is version 1.3 of the entry. See complete history


Role of metals in the biological activity of Clostridium botulinum neurotoxins

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

(2004) Biochemistry 43: 2209-2216

  • DOI: https://doi.org/10.1021/bi035844k
  • Primary Citation of Related Structures:  
    1S0B, 1S0C, 1S0D, 1S0E, 1S0F, 1S0G

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Botulinum neurotoxin type B1,290Clostridium botulinumMutation(s): 0 
Find proteins for P10844 (Clostridium botulinum)
Explore P10844 
Go to UniProtKB:  P10844
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10844
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.05α = 90
b = 122.91β = 113.07
c = 95.43γ = 90
Software Package:
Software NamePurpose
MARMADdata collection
SCALEPACKdata scaling
MARMADdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description