6ES1

Crystal structure of the binding domain from botulinum neurotoxin A2 bound to extracellular domain of human receptor SV2C

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Literature

Crystal Structure of Botulinum Neurotoxin A2 in Complex with the Human Protein Receptor SV2C Reveals Plasticity in Receptor Binding.

Gustafsson, R., Zhang, S., Masuyer, G., Dong, M., Stenmark, P.

(2018) Toxins (Basel) 10

  • DOI: 10.3390/toxins10040153
  • Primary Citation of Related Structures:  
    6ES1

  • PubMed Abstract: 

    • Botulinum neurotoxins (BoNTs) are a family of highly dangerous bacterial toxins, with seven major serotypes (BoNT/A-G). Members of BoNTs, BoNT/A1 and BoNT/B1, have been utilized to treat an increasing number of medical conditions. The clinical trials are ongoing for BoNT/A2, another subtype of BoNT/A, which showed promising therapeutic properties ...

    Botulinum neurotoxins (BoNTs) are a family of highly dangerous bacterial toxins, with seven major serotypes (BoNT/A-G). Members of BoNTs, BoNT/A1 and BoNT/B1, have been utilized to treat an increasing number of medical conditions. The clinical trials are ongoing for BoNT/A2, another subtype of BoNT/A, which showed promising therapeutic properties. Both BoNT/A1 and BoNT/A2 utilize three isoforms of synaptic vesicle protein SV2 (SV2A, B, and C) as their protein receptors. We here present a high resolution (2.0 Å) co-crystal structure of the BoNT/A2 receptor-binding domain in complex with the human SV2C luminal domain. The structure is similar to previously reported BoNT/A-SV2C complexes, but a shift of the receptor-binding segment in BoNT/A2 rotates SV2C in two dimensions giving insight into the dynamic behavior of the interaction. Small differences in key residues at the binding interface may influence the binding to different SV2 isoforms, which may contribute to the differences between BoNT/A1 and BoNT/A2 observed in the clinic.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden. stenmark@dbb.su.se.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Botulinum neurotoxin type AA445Clostridium botulinumMutation(s): 0 
Gene Names: botA, atx, bna
EC: 3.4.24.69
UniProt
Find proteins for Q45894 (Clostridium botulinum (strain Kyoto / Type A2))
Explore Q45894 
Go to UniProtKB:  Q45894
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45894
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptic vesicle glycoprotein 2CB117Homo sapiensMutation(s): 0 
Gene Names: SV2C, KIAA1054
UniProt & NIH Common Fund Data Resources
Find proteins for Q496J9 (Homo sapiens)
Explore Q496J9 
Go to UniProtKB:  Q496J9
PHAROS:  Q496J9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ496J9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.714α = 90
b = 122.108β = 90
c = 47.657γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2014-5667
Wenner-Gren FoundationSweden--
Swedish Cancer SocietySweden--
National Institutes of HealthUnited States1R01NS080833

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release