A single amino acid change in the binding pocket alters specificity of an anti-integrin antibody AP7.4 as revealed by its crystal structure

Monoclonal antibody (mAb) AP7.4 is an anti-integrin antibody recombinantly expressed in Escherichia coli specific to β3. It is known that in a variety of RGD-containing molecules, ligand specificity is regulated by structural determinants within the immediate vicinity of the RGD sequence. To better understand the role of the RGD sequence in integrin specificity, we report here the three-dimensional structure of Fab of mAb AP7.4 to a resolution of 2.25 Å. The crystals belong to a triclinic space group P1 and the volume of the unit cell is consistent with the presence of two Fab molecules in it. The RGD sequence is located at the tip of a flexible loop in the complementary determining region (CDR-3) of the heavy chain. It has been shown that specific recognition of RGD ligands by their receptors is influenced mainly by the conformation of the tripeptide RGD and the amino acid residues flanking it on either side. Hence, the flexibility of the RGD-carrying loop observed in the crystal structure may stem from the fact that the antibody molecule mimics the function of these cell adhesion molecules.