1KC5

CRYSTAL STRUCTURE OF ANTIBODY PC287 IN COMPLEX WITH PS1 PEPTIDE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response.

Nair, D.T., Singh, K., Siddiqui, Z., Nayak, B.P., Rao, K.V., Salunke, D.M.

(2002) J Immunol 168: 2371-2382

  • DOI: 10.4049/jimmunol.168.5.2371
  • Primary Citation of Related Structures:  
    1KC5, 1KCS, 1KCU, 1KCV

  • PubMed Abstract: 

    • Crystal structures of distinct mAbs that recognize a common epitope of a peptide Ag have been determined and analyzed in the unbound and bound forms. These Abs display dissimilar binding site structures in the absence of the Ag. The dissimilarity is primarily expressed in the conformations of complementarity-determining region H3, which is responsible for defining the epitope specificity ...

    Crystal structures of distinct mAbs that recognize a common epitope of a peptide Ag have been determined and analyzed in the unbound and bound forms. These Abs display dissimilar binding site structures in the absence of the Ag. The dissimilarity is primarily expressed in the conformations of complementarity-determining region H3, which is responsible for defining the epitope specificity. Interestingly, however, the three Abs exhibit similar complementarity-determining region conformations in the Ag binding site while recognizing the common epitope, indicating that different pathways of binding are used for Ag recognition. The epitope also exhibits conformational similarity when bound to each of these Abs, although the peptide Ag was otherwise flexible. The observed conformational convergence in the epitope and the Ag binding site was facilitated by the plasticity in the nature of interactions.

    Related Citations: 
    • Crystal Structure of an Antibody Bound to an Immunodominant Peptide Epitope: Novel Features in Peptide-antibody Recognition
      Nair, D.T., Singh, K., Sahu, N., Rao, K.V., Salunke, D.M.
      (2000) J Immunol 165: 6949
    Organizational Affiliation: 

    Structural Biology Unit, National Institute of Immunology, New Delhi 110067, India.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PC287 ImmunoglobulinA [auth L]214Mus musculusMutation(s): 0 
Gene Names: Igkc
UniProt
Find proteins for P01837 (Mus musculus)
Explore P01837 
Go to UniProtKB:  P01837
Entity Groups  
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UniProt GroupP01837
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PC287 ImmunoglobulinB [auth H]217Mus musculusMutation(s): 0 
Gene Names: Ighg1, Igh-4
UniProt
Find proteins for P01869 (Mus musculus)
Explore P01869 
Go to UniProtKB:  P01869
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UniProt GroupP01869
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PS1 peptideC [auth P]15N/AMutation(s): 0 
UniProt
Find proteins for Q91C35 (Hepatitis B virus genotype A1 subtype adw2 (isolate South Africa/84/2001))
Explore Q91C35 
Go to UniProtKB:  Q91C35
Entity Groups  
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UniProt GroupQ91C35
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.59α = 90
b = 71.588β = 98.09
c = 87.677γ = 90
Software Package:
Software NamePurpose
MARdata collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
MARdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance