Kohlschutter-Tönz syndrome(KTS) is a rare autosomal-recessive disease, whose symptoms is epilepsy, global developmental delay, spasticity, and amelogenesis imperfecta. Rogdi is a highly conserved protein across metazoans from worm to human. The structure and function of Rogdi are unknown so far. In general, mutations in Rogdi gene are known as the cause of KTS. In this We suggest the 3-dimentional structure of human Rogdi protein at atomic resolution and correlation between the structure and KTS. The structure of Rogdi consists of α domain and β domain largely. The α domain is internal leucine-zipper like four-helix bundle. The β domain has two β sheet and two short α helices. We determined that α domain is related to the cause of KTS rather than the β domain based on cases of KTS patients. Our biochemical data support that idea. Furthermore, we provide a structural platform for the protein-protein interaction.