In situ architecture of the basal body reveals regionalized assembly and central pair microtubules nucleation

The basal body (BB) is essential for axoneme assembly and ciliary function, and its defects are associated with ciliogenesis disorders and ciliopathies (1,2). However, the molecular basis of the BB's region-specific transitions along the proximal-distal axis, and the mechanism by which ciliary central pair (CP) microtubules are nucleated during ciliogenesis, have remained largely unknown. Here, we resolve the subnanometer architecture of native BBs in mammalian multiciliated cells using cryo-electron tomography and subtomogram averaging, and identify 11 ciliary-base microtubule-associated proteins (CMAPs), including 5 previously uncharacterized core components. These CMAPs localize specifically along ciliary base that facilitate the triplet-to-doublet microtubule transition. We further identify luminal gamma-tubulin ring complexes (gamma-TuRCs) anchored to the microtubule wall via the augmin complex, and propose that they may serve as candidate nucleation sites for CP microtubules biogenesis. Together, these findings define a molecular blueprint of the BB and provide a structural framework for understanding how regional architectural specialization and luminal nucleation collectively drive ciliary assembly and how their dysfunction causes ciliopathies.