Structural determinants of integrin beta-subunit specificity for latent TGF-beta

Eight integrin alpha-beta heterodimers recognize ligands with an Arg-Gly-Asp (RGD) motif. However, the structural mechanism by which integrins differentiate among extracellular proteins with RGD motifs is not understood. Here, crystal structures, mutations and peptide-affinity measurements show that alpha(v)beta(6) binds with high affinity to a RGDLXXL/I motif within the prodomains of TGF-beta 1 and TGF-beta 3. The LXXL/I motif forms an amphipathic alpha-helix that binds in a hydrophobic pocket in the beta(6) subunit. Elucidation of the basis for ligand binding specificity by the integrin beta subunit reveals contributions by three different beta I-domain loops, which we designate specificity-determining loops (SDLs) 1, 2 and 3. Variation in a pair of single key residues in SDL1 and SDL3 correlates with the variation of the entire beta subunit in integrin evolution, thus suggesting a paradigmatic role in overall beta-subunit function.