1BM3

IMMUNOGLOBULIN OPG2 FAB-PEPTIDE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Conformational change in an anti-integrin antibody: structure of OPG2 Fab bound to a beta 3 peptide.

Kodandapani, R.Veerapandian, L.Ni, C.Z.Chiou, C.K.Whittal, R.M.Kunicki, T.J.Ely, K.R.

(1998) Biochem Biophys Res Commun 251: 61-66

  • DOI: 10.1006/bbrc.1998.9380
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Antibodies are important tools to explore receptor-ligand interactions. The anti-integrin antibody OPG2 binds in an RGD-related manner to the alphaIIb beta3 integrin as a molecular mimic of fibrinogen. The Fab fragment from OPG2 was cocrystallized with a peptide from the beta3 subunit of the integrin representing a site that binds RGD ...

    Antibodies are important tools to explore receptor-ligand interactions. The anti-integrin antibody OPG2 binds in an RGD-related manner to the alphaIIb beta3 integrin as a molecular mimic of fibrinogen. The Fab fragment from OPG2 was cocrystallized with a peptide from the beta3 subunit of the integrin representing a site that binds RGD. The crystal structure of the complex was determined at 2.2-A resolution and compared with the unbound Fab. On binding the integrin peptide there were conformational changes in CDR3 of the heavy chain. Also, a significant shift across the intermolecular interface between the CH1-CL domains was observed so that the angle of rotation relating the two domains was reduced by 15 degrees. This unusual conformational adjustment represents the first example of ligand-induced conformational changes in the carboxyl domains of a Fab fragment.


    Related Citations: 
    • Crystal structure of the OPG2 Fab. An antireceptor antibody that mimics an RGD cell adhesion site.
      Kodandapani, R., Veerapandian, B., Kunicki, T.J., Ely, K.R.
      (1995) J Biol Chem 270: 2268

    Organizational Affiliation

    Cancer Research Center, The Burnham Institute, La Jolla, California, 92037, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN OPG2 FAB, CONSTANT DOMAINL214Mus musculusMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN OPG2 FAB, VARIABLE DOMAINH227Mus musculusMutation(s): 0 
Gene Names: Ighg1Igh-4
Find proteins for P01868 (Mus musculus)
Explore P01868 
Go to UniProtKB:  P01868
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.152 
  • Space Group: A 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.11α = 90
b = 90.05β = 115.3
c = 79.11γ = 90
Software Package:
Software NamePurpose
UCSD-systemdata collection
NILSENdata reduction
X-PLORrefinement
UCSD-systemdata reduction
X-GENdata scaling
NILSENdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-20
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2019-11-27
    Changes: Database references