4EN7

Crystal structure of HA70 (HA3) subcomponent of Clostridium botulinum type C progenitor toxin in complex with alpha 2-3-sialyllactosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Carbohydrate recognition mechanism of HA70 from Clostridium botulinum deduced from X-ray structures in complexes with sialylated oligosaccharides

Yamashita, S.Yoshida, H.Uchiyama, N.Nakakita, Y.Nakakita, S.Tonozuka, T.Oguma, K.Nishikawa, A.Kamitori, S.

(2012) FEBS Lett 586: 2404-2410

  • DOI: 10.1016/j.febslet.2012.05.055
  • Primary Citation of Related Structures:  
    4EN6, 4EN7, 4EN8, 4EN9

  • PubMed Abstract: 
  • Clostridium botulinum produces the botulinum neurotoxin, forming a large complex as progenitor toxins in association with non-toxic non-hemagglutinin and/or several different hemagglutinin (HA) subcomponents, HA33, HA17 and HA70, which bind to carbohydrate of glycoproteins from epithelial cells in the infection process ...

    Clostridium botulinum produces the botulinum neurotoxin, forming a large complex as progenitor toxins in association with non-toxic non-hemagglutinin and/or several different hemagglutinin (HA) subcomponents, HA33, HA17 and HA70, which bind to carbohydrate of glycoproteins from epithelial cells in the infection process. To elucidate the carbohydrate recognition mechanism of HA70, X-ray structures of HA70 from type C toxin (HA70/C) in complexes with sialylated oligosaccharides were determined, and a binding assay by the glycoconjugate microarray was performed. These results suggested that HA70/C can recognize both α2-3- and α2-6-sialylated oligosaccharides, and that it has a higher affinity for α2-3-sialylated oligosaccharides.


    Related Citations: 
    • 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

    Organizational Affiliation

    Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Kita-gun, Kagawa 761-0793, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin components HA-22/23/53A224Clostridium botulinumMutation(s): 0 
Gene Names: HA-70
Find proteins for P46085 (Clostridium botulinum C phage)
Explore P46085 
Go to UniProtKB:  P46085
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin components HA-22/23/53B420Clostridium botulinumMutation(s): 0 
Gene Names: HA-70
Find proteins for P46085 (Clostridium botulinum C phage)
Explore P46085 
Go to UniProtKB:  P46085
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC3 N/A Oligosaccharides Interaction
Small Molecules
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900067
Query on PRD_900067
C3'-sialyl-N-acetyllactosamineOligosaccharide /  Substrate analog

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.967α = 90
b = 175.967β = 90
c = 80.753γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary