Structural insights into the function-modulating effects of nanobody binding to the integrin receptor α(M)β(2)

The integrin receptor α(M)β(2) mediates phagocytosis of complement-opsonized objects, adhesion to the extracellular matrix, and transendothelial migration of leukocytes. However, the mechanistic aspects of α(M)β(2) signaling upon ligand binding are unclear. Here, we present the first atomic structure of the human α(M)β(2) headpiece fragment in complex with the nanobody (Nb) hCD11bNb1 at a resolution of 3.2 Å. We show that the receptor headpiece adopts the closed conformation expected to exhibit low ligand affinity. The crystal structure indicates that in the R77H α(M) variant, associated with systemic lupus erythematosus, the modified allosteric relationship between ligand binding and integrin outside–inside signaling is due to subtle conformational effects transmitted over a distance of 40 Å. Furthermore, we found the Nb binds to the αI domain of the α(M) subunit in an Mg(2+)-independent manner with low nanomolar affinity. Biochemical and biophysical experiments with purified proteins demonstrated that the Nb acts as a competitive inhibitor through steric hindrance exerted on the thioester domain of complement component iC3b attempting to bind the α(M) subunit. Surprisingly, we show that the Nb stimulates the interaction of cell-bound α(M)β(2) with iC3b, suggesting that it may represent a novel high-affinity proteinaceous α(M)β(2)-specific agonist. Taken together, our data suggest that the iC3b–α(M)β(2) complex may be more dynamic than predicted from the crystal structure of the core complex. We propose a model based on the conformational spectrum of the receptor to reconcile these observations regarding the functional consequences of hCD11bNb1 binding to α(M)β(2).