8AGK

Botulinum neurotoxin subtype A6 cell binding domain in complex with GD1a ganglioside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structures of the Clostridium botulinum Neurotoxin A6 Cell Binding Domain Alone and in Complex with GD1a Reveal Significant Conformational Flexibility.

Gregory, K.S.Newell, A.R.Mojanaga, O.O.Liu, S.M.Acharya, K.R.

(2022) Int J Mol Sci 23

  • DOI: https://doi.org/10.3390/ijms23179620
  • Primary Citation of Related Structures:  
    8AGK, 8ALP

  • PubMed Abstract: 

    Clostridium botulinum neurotoxin A (BoNT/A) targets the soluble N -ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, by cleaving synaptosomal-associated protein of 25 kDa size ( SNAP - 25 ). Cleavage of SNAP-25 results in flaccid paralysis due to repression of synaptic transmission at the neuromuscular junction. This activity has been exploited to treat a range of diseases associated with hypersecretion of neurotransmitters, with formulations of BoNT/A commercially available as therapeutics. Generally, BoNT activity is facilitated by three essential domains within the molecule, the cell binding domain (H C ), the translocation domain (H N ), and the catalytic domain (LC). The H C, which consists of an N-terminal (H CN ) and a C-terminal (H CC ) subdomain, is responsible for BoNT's high target specificity where it forms a dual-receptor complex with synaptic vesicle protein 2 (SV2) and a ganglioside receptor on the surface of motor neurons. In this study, we have determined the crystal structure of botulinum neurotoxin A6 cell binding domain (H C /A6) in complex with GD1a and describe the interactions involved in ganglioside binding. We also present a new crystal form of wild type H C /A6 (crystal form II) where a large 'hinge motion' between the H CN and H CC subdomains is observed. These structures, along with a comparison to the previously determined wild type crystal structure of H C /A6 (crystal form I), reveals the degree of conformational flexibility exhibited by H C /A6.


  • Organizational Affiliation

    Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bont/A1A [auth AAA]433Clostridium botulinum str. Iwanei EMutation(s): 0 
UniProt
Find proteins for C9WWY7 (Clostridium botulinum)
Explore C9WWY7 
Go to UniProtKB:  C9WWY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC9WWY7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-alpha-D-glucopyranoseB [auth BBB]5N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.307α = 90
b = 83.636β = 98.659
c = 58.313γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description