2ZS6

HA3 subcomponent of botulinum type C progenitor toxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the HA3 Subcomponent of Clostridium botulinum Type C Progenitor Toxin

Nakamura, T.Kotani, M.Tonozuka, T.Ide, A.Oguma, K.Nishikawa, A.

(2009) J.Mol.Biol. 385: 1193-1206

  • DOI: 10.1016/j.jmb.2008.11.039
  • Primary Citation of Related Structures:  
  • Also Cited By: 4EN9, 4EN8, 4EN7, 4EN6

  • PubMed Abstract: 
  • The Clostridium botulinum type C 16S progenitor toxin contains a neurotoxin and several nontoxic components, designated nontoxic nonhemagglutinin (HA), HA1 (HA-33), HA2 (HA-17), HA3a (HA-22-23), and HA3b (HA-53). The HA3b subcomponent seems to play a ...

    The Clostridium botulinum type C 16S progenitor toxin contains a neurotoxin and several nontoxic components, designated nontoxic nonhemagglutinin (HA), HA1 (HA-33), HA2 (HA-17), HA3a (HA-22-23), and HA3b (HA-53). The HA3b subcomponent seems to play an important role cooperatively with HA1 in the internalization of the toxin by gastrointestinal epithelial cells via binding of these subcomponents to specific oligosaccharides. In this study, we investigated the sugar-binding specificity of the HA3b subcomponent using recombinant protein fused to glutathione S-transferase and determined the three-dimensional structure of the HA3a-HA3b complex based on X-ray crystallography. The crystal structure was determined at a resolution of 2.6 A. HA3b contains three domains, domains I to III, and the structure of domain I resembles HA3a. In crystal packing, three HA3a-HA3b molecules are assembled to form a three-leaved propeller-like structure. The three HA3b domain I and three HA3a alternate, forming a trimer of dimers. In a database search, no proteins with high structural homology to any of the domains (Z score >10) were found. Especially, HA3a and HA3b domain I, mainly composed of beta-sheets, reveal a unique fold. In binding assays, HA3b bound sialic acid with high affinity, but did not bind galactose, N-acetylgalactosamine, or N-acetylglucosamine. The electron density of liganded N-acetylneuraminic acid was determined by crystal soaking. In the sugar-complex structure, the N-acetylneuraminic acid-binding site was located in the cleft formed between domains II and III of HA3b. This report provides the first determination of the three-dimensional structure of the HA3a-HA3b complex and its sialic acid binding site. Our results will provide useful information for elucidating the mechanism of assembly of the C16S toxin and for understanding the interactions with oligosaccharides on epithelial cells and internalization of the botulinum toxin complex.


    Related Citations: 
    • Sugar-binding sites of the HA1 subcomponent of Clostridium botulinum type C progenitor toxin.
      Nakamura, T.,Tonozuka, T.,Ide, A.,Yuzawa, T.,Oguma, K.,Nishikawa, A.
      (2008) J.Mol.Biol. 376: 854
    • Binding properties of Clostridium botulinum type C progenitor toxin to mucins.
      Nakamura, T.,Takada, N.,Tonozuka, T.,Sakano, Y.,Oguma, K.,Nishikawa, A.
      (2007) Biochim.Biophys.Acta 1770: 551


    Organizational Affiliation

    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin components HA3
A
205Clostridium botulinumMutation(s): 0 
Gene Names: HA-70 (antP-70)
Find proteins for P46085 (Clostridium botulinum)
Go to UniProtKB:  P46085
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin components HA3
B
420Clostridium botulinumMutation(s): 0 
Gene Names: HA-70 (antP-70)
Find proteins for P46085 (Clostridium botulinum)
Go to UniProtKB:  P46085
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.222 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 176.397α = 90.00
b = 176.397β = 90.00
c = 80.911γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSphasing
CNSrefinement
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance