4JRA

CRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING DOMAIN IN COMPLEX WITH THE LUMINAL DOMAIN Of SV2C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for recognition of synaptic vesicle protein 2C by botulinum neurotoxin A.

Benoit, R.M.Frey, D.Hilbert, M.Kevenaar, J.T.Wieser, M.M.Stirnimann, C.U.McMillan, D.Ceska, T.Lebon, F.Jaussi, R.Steinmetz, M.O.Schertler, G.F.Hoogenraad, C.C.Capitani, G.Kammerer, R.A.

(2014) Nature 505: 108-111

  • DOI: 10.1038/nature12732

  • PubMed Abstract: 
  • Botulinum neurotoxin A (BoNT/A) belongs to the most dangerous class of bioweapons. Despite this, BoNT/A is used to treat a wide range of common medical conditions such as migraines and a variety of ocular motility and movement disorders. BoNT/A is pr ...

    Botulinum neurotoxin A (BoNT/A) belongs to the most dangerous class of bioweapons. Despite this, BoNT/A is used to treat a wide range of common medical conditions such as migraines and a variety of ocular motility and movement disorders. BoNT/A is probably best known for its use as an antiwrinkle agent in cosmetic applications (including Botox and Dysport). BoNT/A application causes long-lasting flaccid paralysis of muscles through inhibiting the release of the neurotransmitter acetylcholine by cleaving synaptosomal-associated protein 25 (SNAP-25) within presynaptic nerve terminals. Two types of BoNT/A receptor have been identified, both of which are required for BoNT/A toxicity and are therefore likely to cooperate with each other: gangliosides and members of the synaptic vesicle glycoprotein 2 (SV2) family, which are putative transporter proteins that are predicted to have 12 transmembrane domains, associate with the receptor-binding domain of the toxin. Recently, fibroblast growth factor receptor 3 (FGFR3) has also been reported to be a potential BoNT/A receptor. In SV2 proteins, the BoNT/A-binding site has been mapped to the luminal domain, but the molecular details of the interaction between BoNT/A and SV2 are unknown. Here we determined the high-resolution crystal structure of the BoNT/A receptor-binding domain (BoNT/A-RBD) in complex with the SV2C luminal domain (SV2C-LD). SV2C-LD consists of a right-handed, quadrilateral β-helix that associates with BoNT/A-RBD mainly through backbone-to-backbone interactions at open β-strand edges, in a manner that resembles the inter-strand interactions in amyloid structures. Competition experiments identified a peptide that inhibits the formation of the complex. Our findings provide a strong platform for the development of novel antitoxin agents and for the rational design of BoNT/A variants with improved therapeutic properties.


    Organizational Affiliation

    Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Botulinum neurotoxin type A
A, B
443Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)Mutation(s): 0 
Gene Names: botA (bna)
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A))
Go to UniProtKB:  P0DPI1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Synaptic vesicle glycoprotein 2C
C, D
136Homo sapiensMutation(s): 0 
Gene Names: SV2C (KIAA1054)
Find proteins for Q496J9 (Homo sapiens)
Go to Gene View: SV2C
Go to UniProtKB:  Q496J9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.440α = 90.00
b = 105.260β = 90.02
c = 127.960γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2013-11-27
    Type: Database references
  • Version 1.2: 2014-02-12
    Type: Database references