1PLG

EVIDENCE FOR THE EXTENDED HELICAL NATURE OF POLYSACCHARIDE EPITOPES. THE 2.8 ANGSTROMS RESOLUTION STRUCTURE AND THERMODYNAMICS OF LIGAND BINDING OF AN ANTIGEN BINDING FRAGMENT SPECIFIC FOR ALPHA-(2->8)-POLYSIALIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Evidence for the extended helical nature of polysaccharide epitopes. The 2.8 A resolution structure and thermodynamics of ligand binding of an antigen binding fragment specific for alpha-(2-->8)-polysialic acid.

Evans, S.V.Sigurskjold, B.W.Jennings, H.J.Brisson, J.R.To, R.Tse, W.C.Altman, E.Frosch, M.Weisgerber, C.Kratzin, H.D.Klebert, S.Vaesen, M.Bitter-Suermann, D.Rose, D.R.Young, N.M.Bundle, D.R.

(1995) Biochemistry 34: 6737-6744

  • DOI: 10.1021/bi00020a019
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The antigen binding fragment from an IgG2a kappa murine monoclonal antibody with specificity for alpha-(2-->8)-linked sialic acid polymers has been prepared and crystallized in the absence of hapten. Crystals were grown by vapor diffusion equilibrium ...

    The antigen binding fragment from an IgG2a kappa murine monoclonal antibody with specificity for alpha-(2-->8)-linked sialic acid polymers has been prepared and crystallized in the absence of hapten. Crystals were grown by vapor diffusion equilibrium with 16-18% polyethylene glycol 4000 solutions. The structure was solved by molecular replacement methods and refined to a conventional R factor of 0.164 for data to 2.8 A. The binding site is observed to display a shape and distribution of charges that is complementary to that of the predicted conformation of the oligosaccharide epitope. A thermodynamic description of ligand binding has been compiled for oligosaccharides ranging in length from 9 to 41 residues, and the data for the largest ligand has been used in a novel way to estimate the size of the antigen binding site. A model of antigen binding is presented that satisfies this thermodynamic data, as well as a previously reported requirement of conformational specificity of the oligosaccharide. X-ray crystallographic and thermodynamic evidence are consistent with a binding site that accommodates at least eight sialic acid residues.


    Related Citations: 
    • Helical Epitope of the Group B Meningococcal Alpha(2->8)-Linked Sialic Acid Polysaccharide
      Brisson, J.-R., Baumann, H., Imberty, A., Perez, S., Jennings, H.J.
      (1992) Biochemistry 31: 4996

    Organizational Affiliation

    Institute for Biological Sciences, National Research Council of Canada, Ottawa.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2A=KAPPA=L215Mus musculusMutation(s): 0 
Gene Names: IgkcIgk-C
Find proteins for A2NHM3 (Mus musculus)
Explore A2NHM3 
Go to UniProtKB:  A2NHM3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A=KAPPA=H215Mus musculusMutation(s): 0 
Gene Names: Igh-1a
Find proteins for P01865 (Mus musculus)
Explore P01865 
Go to UniProtKB:  P01865
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.14α = 90
b = 91.21β = 90
c = 141.4γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-02-22
    Changes: Database references