4EN6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 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: https://doi.org/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. 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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin components HA-22/23/53224Clostridium botulinumMutation(s): 0 
Gene Names: HA-70
UniProt
Find proteins for P46085 (Clostridium botulinum C phage)
Explore P46085 
Go to UniProtKB:  P46085
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46085
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin components HA-22/23/53420Clostridium botulinumMutation(s): 0 
Gene Names: HA-70
UniProt
Find proteins for P46085 (Clostridium botulinum C phage)
Explore P46085 
Go to UniProtKB:  P46085
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46085
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
C
3N/A
Glycosylation Resources
GlyTouCan:  G91237TK
GlyCosmos:  G91237TK
GlyGen:  G91237TK
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.596α = 90
b = 175.596β = 90
c = 80.779γ = 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
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary