1YYN

A common binding site for disialyllactose and a tri-peptide in the C-fragment of tetanus neurotoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Common binding site for disialyllactose and tri-peptide in C-fragment of tetanus neurotoxin

Jayaraman, S.Eswaramoorthy, S.Kumaran, D.Swaminathan, S.

(2005) Proteins 61: 288-295

  • DOI: 10.1002/prot.20595
  • Primary Citation of Related Structures:  
    1YYN, 1YXW

  • PubMed Abstract: 
  • Clostridial neurotoxins are comprised of botulinum (BoNT) and tetanus (TeNT), which share significant structural and functional similarity. Crystal structures of the binding domain of TeNT complexed with disialyllactose (DiSia) and a tri-peptide Tyr-Glu-Trp (YEW) have been determined to 2 ...

    Clostridial neurotoxins are comprised of botulinum (BoNT) and tetanus (TeNT), which share significant structural and functional similarity. Crystal structures of the binding domain of TeNT complexed with disialyllactose (DiSia) and a tri-peptide Tyr-Glu-Trp (YEW) have been determined to 2.3 and 2.2 A, respectively. Both DiSia and YEW bind in a shallow cleft region on the surface of the molecule in the beta-trefoil domain, interacting with a set of common residues, Asp1147, Asp1214, Asn1216, and Arg1226. DiSia and YEW binding at the same site in tetanus toxin provides a putative site that could be occupied either by a ganglioside moiety or a peptide. Soaking experiments with a mixture of YEW and DiSia show that YEW competes with DiSia, suggesting that YEW can be used to block ganglioside binding. A comparison with the TeNT binding domain in complex with small molecules, BoNT/A and /B, provides insight into the different modes of ganglioside binding.


    Organizational Affiliation

    Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tetanus toxinA441Clostridium tetaniMutation(s): 0 
EC: 3.4.24.68
UniProt
Find proteins for P04958 (Clostridium tetani (strain Massachusetts / E88))
Explore P04958 
Go to UniProtKB:  P04958
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-beta-D-glucopyranoseB4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G74861PZ
GlyCosmos:  G74861PZ
GlyGen:  G74861PZ
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.907α = 90
b = 78.93β = 90
c = 90.977γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CBASSdata collection
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary