1DVF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249 
  • R-Value Work: 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

  • 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: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FV D1.3
A
108Mus musculusN/A
Find proteins for P01635 (Mus musculus)
Go to UniProtKB:  P01635
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FV D1.3
B
116Mus musculusN/A
Find proteins for P01820 (Mus musculus)
Go to UniProtKB:  P01820
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FV E5.2
C
107Mus musculusN/A
Find proteins for P01646 (Mus musculus)
Go to UniProtKB:  P01646
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
FV E5.2
D
121Mus musculusN/A
Find proteins for A0NA69 (Mus musculus)
Go to UniProtKB:  A0NA69
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 152.800α = 90.00
b = 79.400β = 100.20
c = 51.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
XENGENdata reduction
XENGENdata collection
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model