Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48058.29 
• Atom Count: 3276 
• Residue Count: 441 
• Unique protein chains: 2

1BM3

IMMUNOGLOBULIN OPG2 FAB-PEPTIDE COMPLEX

• DOI: 10.2210/pdb1BM3/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus


• Deposited: 1999-04-15 Released: 1999-04-20 
• Deposition Author(s): Kodandapani, R., Veerapandian, L., Ni, C.Z., Chiou, C.-K., Whital, R., Kunicki, T.J., Ely, K.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.152 

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

• PubMed: 9790907 
• DOI: 10.1006/bbrc.1998.9380


• 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. 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.

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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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
IMMUNOGLOBULIN OPG2 FAB, CONSTANT DOMAIN	L	214	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
IMMUNOGLOBULIN OPG2 FAB, VARIABLE DOMAIN	H	227	Mus musculus	Mutation(s): 0  Gene Names: Ighg1 (Igh-4)
Find proteins for P01868 (Mus musculus) Go to UniProtKB:  P01868

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.152 
• Space Group: A 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 74.110	α = 90.00
b = 90.050	β = 115.30
c = 79.110	γ = 90.00

Software Package:

Software Name	Purpose
X-GEN	data scaling
NILSEN	data reduction
X-PLOR	refinement
UCSD-system	data reduction
NILSEN	data scaling
UCSD-system	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-04-15 
• Released Date: 1999-04-20 
• Deposition Author(s): Kodandapani, R., Veerapandian, L., Ni, C.Z., Chiou, C.-K., Whital, R., Kunicki, T.J., Ely, K.R.

Revision History 

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