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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.febslet.2012.05.055
  • Primary Citation of Related Structures:  

  • 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 carboh ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin components HA-22/23/53
A
224Clostridium botulinum C phageMutation(s): 0 
Gene Names: HA-70 (antP-70, cha-70)
Find proteins for P46085 (Clostridium botulinum C phage)
Go to UniProtKB:  P46085
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin components HA-22/23/53
B
420Clostridium botulinum C phageMutation(s): 0 
Gene Names: HA-70 (antP-70, cha-70)
Find proteins for P46085 (Clostridium botulinum C phage)
Go to UniProtKB:  P46085
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download SDF File 
Download CCD File 
A, B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
B
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 175.967α = 90.00
b = 175.967β = 90.00
c = 80.753γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
HKL-2000data collection
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references