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 

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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: https://doi.org/10.1021/bi00020a019
  • Primary Citation of Related Structures:  
    1PLG

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IGG2A=KAPPA=A [auth L]215Mus musculusMutation(s): 0 
UniProt
Find proteins for A2NHM3 (Mus musculus)
Explore A2NHM3 
Go to UniProtKB:  A2NHM3
Entity Groups  
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UniProt GroupA2NHM3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IGG2A=KAPPA=B [auth H]215Mus musculusMutation(s): 0 
UniProt
Find proteins for P01865 (Mus musculus)
Explore P01865 
Go to UniProtKB:  P01865
Entity Groups  
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UniProt GroupP01865
Sequence Annotations
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  • 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

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Entry History 

Revision History  (Full details and data files)

  • 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