3OBR

Crystal structure of Botulinum neurotoxin serotype D binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.129 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Botulinum neurotoxin serotype D attacks neurons via two carbohydrate-binding sites in a ganglioside-dependent manner.

Strotmeier, J.Lee, K.Volker, A.K.Mahrhold, S.Zong, Y.Zeiser, J.Zhou, J.Pich, A.Bigalke, H.Binz, T.Rummel, A.Jin, R.

(2010) Biochem J 431: 207-216

  • DOI: https://doi.org/10.1042/BJ20101042
  • Primary Citation of Related Structures:  
    3OBR, 3OBT

  • PubMed Abstract: 

    The extraordinarily high toxicity of botulinum neurotoxins primarily results from their specific binding and uptake into neurons. At motor neurons, the seven BoNT (botulinum neurotoxin) serotypes A-G inhibit acetylcholine release leading to flaccid paralysis. Uptake of BoNT/A, B, E, F and G requires a dual interaction with gangliosides and the synaptic vesicle proteins synaptotagmin or SV2 (synaptic vesicle glycoprotein 2), whereas little is known about the cell entry mechanisms of the serotypes C and D, which display the lowest amino acid sequence identity compared with the other five serotypes. In the present study we demonstrate that the neurotoxicity of BoNT/D depends on the presence of gangliosides by employing phrenic nerve hemidiaphragm preparations derived from mice expressing the gangliosides GM3, GM2, GM1 and GD1a, or only GM3 [a description of our use of ganglioside nomenclature is given in Svennerholm (1994) Prog. Brain Res. 101, XI-XIV]. High-resolution crystal structures of the 50 kDa cell-binding domain of BoNT/D alone and in complex with sialic acid, as well as biological analyses of single-site BoNT/D mutants identified two carbohydrate-binding sites. One site is located at a position previously identified in BoNT/A, B, E, F and G, but is lacking the conserved SXWY motif. The other site, co-ordinating one molecule of sialic acid, resembles the second ganglioside-binding pocket (the sialic-acid-binding site) of TeNT (tetanus neurotoxin).


  • Organizational Affiliation

    Institut für Toxikologie, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, Hannover, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Botulinum neurotoxin type D434Clostridium botulinumMutation(s): 0 
Gene Names: botD
EC: 3.4.24.69
UniProt
Find proteins for P19321 (Clostridium botulinum D phage)
Explore P19321 
Go to UniProtKB:  P19321
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19321
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.129 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.677α = 90
b = 89.871β = 90
c = 94.117γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-04-16
    Changes: Other