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Rootletin is the main component of the ciliary rootlet and functions as a centriole linker connecting the two mother centrioles. Despite the functional importance of rootletin, the molecular architecture of the rootletin filament and its assembly mechanism are poorly understood. Here, we identify the coiled-coil domain 3 (CCD3) of rootletin as the key domain for its cellular function. The crystal structure of the CCD31108-1317 fragment containing 28 heptad repeats and one hendecad repeat reveals that it forms a parallel coiled-coil dimer