1BM3 | pdb_00001bm3

IMMUNOGLOBULIN OPG2 FAB-PEPTIDE COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1BM3/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• 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: 2.00 Å
• R-Value Work: 
  0.152 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1006/bbrc.1998.9380
• Primary Citation Related Structures: 
  1BM3


• 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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Organizational Affiliation: 
• Cancer Research Center, The Burnham Institute, La Jolla, California, 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 48.06 kDa 
• Atom Count: 3,589 
• Modeled Residue Count: 430 
• Deposited Residue Count: 441 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN OPG2 FAB, CONSTANT DOMAIN	A [auth L]	214	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN OPG2 FAB, VARIABLE DOMAIN	B [auth H]	227	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01868 (Mus musculus) Explore P01868  Go to UniProtKB:  P01868

Experimental Data & Validation

Experimental Data

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

Space Group: A 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.11	α = 90
b = 90.05	β = 115.3
c = 79.11	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  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
• Version 1.5: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2024-10-30
  Changes: Structure summary