1XTG

Crystal structure of NEUROTOXIN BONT/A complexed with Synaptosomal-associated protein 25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Substrate recognition strategy for botulinum neurotoxin serotype A

Breidenbach, M.A.Brunger, A.T.

(2004) Nature 432: 925-929

  • DOI: 10.1038/nature03123
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clostridal neurotoxins (CNTs) are the causative agents of the neuroparalytic diseases botulism and tetanus. CNTs impair neuronal exocytosis through specific proteolysis of essential proteins called SNAREs. SNARE assembly into a low-energy ternary com ...

    Clostridal neurotoxins (CNTs) are the causative agents of the neuroparalytic diseases botulism and tetanus. CNTs impair neuronal exocytosis through specific proteolysis of essential proteins called SNAREs. SNARE assembly into a low-energy ternary complex is believed to catalyse membrane fusion, precipitating neurotransmitter release; this process is attenuated in response to SNARE proteolysis. Site-specific SNARE hydrolysis is catalysed by the CNT light chains, a unique group of zinc-dependent endopeptidases. The means by which a CNT properly identifies and cleaves its target SNARE has been a subject of much speculation; it is thought to use one or more regions of enzyme-substrate interaction remote from the active site (exosites). Here we report the first structure of a CNT endopeptidase in complex with its target SNARE at a resolution of 2.1 A: botulinum neurotoxin serotype A (BoNT/A) protease bound to human SNAP-25. The structure, together with enzyme kinetic data, reveals an array of exosites that determine substrate specificity. Substrate orientation is similar to that of the general zinc-dependent metalloprotease thermolysin. We observe significant structural changes near the toxin's catalytic pocket upon substrate binding, probably serving to render the protease competent for catalysis. The novel structures of the substrate-recognition exosites could be used for designing inhibitors specific to BoNT/A.


    Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEUROTOXIN BONT/A
A
424Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)Mutation(s): 2 
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
Synaptosomal-associated protein 25
B
59Homo sapiensMutation(s): 0 
Gene Names: SNAP25 (SNAP)
Find proteins for P60880 (Homo sapiens)
Go to Gene View: SNAP25
Go to UniProtKB:  P60880
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-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: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 86.000α = 90.00
b = 86.000β = 90.00
c = 165.400γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Advisory, Experimental preparation