Guanylate-kinase-associated protein (GKAP) is a scaffolding protein that links NMDA receptor-PSD-95 to Shank-Homer complexes by protein-protein interactions at the synaptic junction. GKAP family proteins are characterized by the presence of a C-terminal conserved GKAP homology domain 1 (GH1) of unknown structure and function. In this study. crystal structure of the GHl domain of GKAP from Rattus norvegicus was determined in fusion with an N-terminal maltose-binding protein at 2.0 A resolution. The structure of GKAP GHl displays a three-helix bundle connected by short flexible loops. The predicted helix ot4 which was not visible in the crystal structure associates weakly with the helix ot3 suggesting dynamic nature of the GHl domain. The strict conservation of GHl domain across GKAP family members and the lack of a catalytic active site required for enzyme activity imply that the GHl domain might serve as a protein-protein interaction module for the synaptic protein clustering. ⓒ 2014 Elsevier Inc. All rights reserved.