1DVF

IDIOTOPIC ANTIBODY D1.3 FV FRAGMENT-ANTIIDIOTOPIC ANTIBODY E5.2 FV FRAGMENT COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of an Fv-Fv idiotope-anti-idiotope complex at 1.9 A resolution.

Braden, B.C.Fields, B.A.Ysern, X.Dall'Acqua, W.Goldbaum, F.A.Poljak, R.J.Mariuzza, R.A.

(1996) J Mol Biol 264: 137-151

  • DOI: 10.1006/jmbi.1996.0629
  • Primary Citation of Related Structures:  
    1DVF

  • PubMed Abstract: 
  • Anti-idiotopic antibodies react with unique antigenic features, usually associated with the combining sites, of other antibodies. They may thus mimic specific antigens that react with the same antibodies. The structural basis of this mimicry is analy ...

    Anti-idiotopic antibodies react with unique antigenic features, usually associated with the combining sites, of other antibodies. They may thus mimic specific antigens that react with the same antibodies. The structural basis of this mimicry is analyzed here in detail for an anti-idiotopic antibody that mimics the antigen, hen egg-white lysozyme. The crystal structure of an anti-hen-egg-white lysozyme antibody (D1.3) complexed with an anti-idiotopic antibody (E5.2) has been determined at a nominal resolution of 1.9 A. E5.2 contacts substantially the same residues of D1.3 as lysozyme, thus mimicking its binding to D1.3. The mimicry embodies conservation of hydrogen bonding: six of the 14 protein-protein hydrogen bonds bridging D1.3-E5.2 are structurally equivalent to hydrogen bonds bridging D1.3-lysozyme. The mimicry includes a similar number of van der Waals interactions. The mimicry of E5.2 for lysozyme, however, does not extend to the topology of the non-polar surfaces of E5.2 and lysozyme, which are in contact with D1.3 as revealed by a quantitative analysis of the contacting surface similarities between E5.2 and lysozyme. The structure discussed herein shows that an anti-idiotopic antibody can provide an approximate topological and binding-group mimicry of an external antigen, especially in the case of the hydrophilic surfaces, even though there is no sequence homology between the anti-idiotope and the antigen.


    Related Citations: 
    • Molecular Basis of Antigen Mimicry by an Anti-Idiotope
      Fields, B.A., Goldbaum, F.A., Ysern, X., Poljak, R.J., Mariuzza, R.A.
      (1995) Nature 374: 739
    • Crystallization and Preliminary X-Ray Diffraction Study of an Idiotope-Anti-Idiotope Fv-Fv Complex
      Goldbaum, F.A., Fields, B.A., Cauerhff, A., Ysern, X., Houdusse, A., Eisele, J.L., Poljak, R.J., Mariuzza, R.A.
      (1994) J Mol Biol 241: 739

    Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville 20850, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FV D1.3A108Mus musculusMutation(s): 0 
Find proteins for P01635 (Mus musculus)
Explore P01635 
Go to UniProtKB:  P01635
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FV D1.3B116Mus musculusMutation(s): 0 
Find proteins for P01820 (Mus musculus)
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Go to UniProtKB:  P01820
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FV E5.2C107Mus musculusMutation(s): 0 
Find proteins for P01646 (Mus musculus)
Explore P01646 
Go to UniProtKB:  P01646
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
FV E5.2D121Mus musculusMutation(s): 0 
Find proteins for A0NA69 (Mus musculus)
Explore A0NA69 
Go to UniProtKB:  A0NA69
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.8α = 90
b = 79.4β = 100.2
c = 51.5γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-17
    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: 2011-11-16
    Changes: Atomic model