Tight junctions are dynamic components of epithelial and endothelial cells that regulate the paracellular transport of ions, solutes, and immune cells. The assembly and permeability of these junctions is dependent on the zonula occludens (ZO) proteins, members of the membrane-associated guanylate kinase homolog (MAGUK) protein family, which are characterized by a core Src homology 3 (SH3)-GUK module that coordinates multiple protein-protein interactions. The structure of the ZO-1 SH3-GUK domain confirms that the interdependent folding of the SH3 and GUK domains is a conserved feature of MAGUKs, but differences in the orientation of the GUK domains in three different MAGUKs reveal interdomain flexibility of the core unit. Using pull-down assays, we show that an effector loop, the U6 region in ZO-1, forms a novel intramolecular interaction with the core module. This interaction is divalent cation-dependent and overlaps with the binding site for the regulatory molecule calmodulin on the GUK domain. These findings provide insight into the previously observed ability of the U6 region to regulate TJ assembly in vivo and the structural basis for the complex protein interactions of the MAGUK family.The assembly and functional organization of plasma membrane domains, such as synapses and cell adhesions, depends on the temporally and spatially regulated assembly of multiprotein complexes. In one common paradigm, the trafficking and assembly of the transmembrane receptors and adhesion molecules that form these complexes is organized by a series of cytosolic scaffolding proteins. One of the most common and ubiquitous families of scaffolding molecules is the membraneassociated guanylate kinase homologs (MAGUKs).2 Founding members of this family include the discs large tumor suppressor in Drosophila, Lin2, which is required for RT kinase signaling in Caenorhabditis and PSD-95 and its related synaptic scaffolding proteins, which also control channel activity. This diverse family of proteins is characterized by a core motif of protein-binding domains, including a PSD-95/DLG/ZO-1 (PDZ) domain, an Src homology 3 (SH3) domain, and a region of homology to guanylate kinase referred to as the GUK domain ( Fig. 1A) (reviewed in Ref. 1). Most also include additional PDZ domains or other conserved protein-binding domains. These domains are separated by unique regions (U regions), which can also have protein-binding and regulatory roles (1, 2). However, it is the core SH3-GUK module and its adjacent unique domains that often have a dominant role in the regulation of transmembrane ligand binding, protein cross-linking, and localization to the appropriate subcellular domain.The structural basis for the regulatory properties of the various MAGUKs is poorly understood. To date, the only core motif that has been resolved at an atomic level belongs to PSD-95 (postsynaptic density protein 95) (3, 4), a neuronal protein involved in the regulation of postsynaptic gated ion channel. The structure reveals that the SH3 and GUK domains are not simply...