Since the discovery of the RGD sequence motif as the essential cell attachment site in Fn (fibronectin), RGD-dependent ligand recognition by integrins has been the major focus of many integrin researches. Although many integrins recognize RGD-containing ligands, it is believed that residues outside the RGD motif provide specificity as well as high affinity for each integrin–ligand pair. These ‘secondary’ sites are generally assumed to interact directly with the α subunit of integrin, whereas the RGD motif binds primarily to the β subunit. This necessitates that the integrin–ligand interface comprises a relatively large, or even scattered, area. Molecular electron microscopy and single-particle analysis were performed on a headpiece fragment of integrin α5β1 in the presence and absence of bound ligand (Fn fragment), and revealed a marked shape change of the β subunit hybrid and I-like domains that is linked with the ligand docking. Furthermore, electron microscopy images revealed a focal rather than a large contact area at the α5β1–Fn interface, raising a question about ‘2-site docking model’. Kinetic analysis of real-time binding data showed that the synergy site greatly enhances kon but has little effect on the stability or koff of the complex, suggesting that the synergy site exerts its positive effect on α5β1 binding by facilitating the initial encounter, rather than by contributing to the protein–protein interaction surface. Thus the ligand recognition mechanism by integrins needs further refinement through more structural analyses of the complexes as well as kinetic analysis of binding data.