1DBK

MOLECULAR BASIS OF CROSS-REACTIVITY AND THE LIMITS OF ANTIBODY-ANTIGEN COMPLEMENTARITY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis of crossreactivity and the limits of antibody-antigen complementarity.

Arevalo, J.H.Taussig, M.J.Wilson, I.A.

(1993) Nature 365: 859-863

  • DOI: 10.1038/365859a0
  • Primary Citation of Related Structures:  
    1DBM, 1DBK, 1DBJ, 2DBL

  • PubMed Abstract: 
  • Two major unanswered questions concerning the specificity of antibodies are: how do structurally different antigens bind with high affinity to the same antibody, and what are the limits of the antibody combining site complementarity and flexibility t ...

    Two major unanswered questions concerning the specificity of antibodies are: how do structurally different antigens bind with high affinity to the same antibody, and what are the limits of the antibody combining site complementarity and flexibility that contribute to such crossreactivity? We report here a comparative analysis of the X-ray structures of five conformationally different steroids in complex with the Fab' fragment of an anti-progesterone antibody DB3 at 2.7 A. This antibody is unable to complement completely the shape of the hydrophobic antigen so that crossreactivity occurs with other ligands without major structural rearrangements of the binding site. Antigen specificity can be explained through conserved interactions of DB3 with the steroid D-ring, whereas some of the crossreactivity is realized through different binding orientations of the steroid skeleton that place the A-ring into alternative pockets on the antibody surface. The restricted gene usage of the VGAM3.8 family in the generation of anti-progesterone monoclonal antibodies may be explained by the specific interaction of VH hallmark residues with the steroid D-ring. This first detailed structure of steroid interactions with a protein could be applied to the understanding of general mechanisms of steroid recognition as well as in the design of specific binding sites for small hydrophobic ligands.


    Related Citations: 
    • Structural Analysis of Antibody Specificity: Detailed Comparison of Five Fab'-Steroid Complexes
      Arevalo, J.H., Hassig, C.A., Stura, E.A., Taussig, M.J., Wilson, I.A.
      () To be published --: --
    • Three-Dimensional Structure of an Anti-Steroid Fab' and Progesterone-Fab' Complex
      Arevalo, J.H., Stura, E.A., Taussig, M.J., Wilson, I.A.
      (1993) J Mol Biol 231: 103
    • Analysis of an Anti-Progesterone Antibody: Variable Crystal Morphology of the Fab' and Steroid-Fab' Complexes
      Stura, E.A., Arevalo, J.H., Feinstein, A., Heap, R.B., Taussig, M.J., Wilson, I.A.
      (1987) Immunology 62: 511

    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGG1-KAPPA DB3 FAB (LIGHT CHAIN)L216Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGG1-KAPPA DB3 FAB (HEAVY CHAIN)H219Mus musculusMutation(s): 0 
Gene Names: Ighg1Igh-4
Find proteins for P01868 (Mus musculus)
Explore P01868 
Go to UniProtKB:  P01868
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANO
Query on ANO

Download CCD File 
H
5-BETA-ANDROSTANE-3,17-DIONE
C19 H28 O2
RAJWOBJTTGJROA-QJISAEMRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ANOIC50 :  8   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.76α = 90
b = 134.76β = 90
c = 124.21γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance