A pair of extensively modified microtubules form the central apparatus (CA) of the axoneme of most motile cilia, where they regulate ciliary motility. The external surfaces of both CA microtubules are patterned asymmetrically with large protein complexes that repeat every 16 or 32 nm. The composition of these projections and the mechanisms that establish asymmetry and longitudinal periodicity are unknown. Here, by determining cryo-EM structures of the CA microtubules, we identify 48 different CA-associated proteins, which in turn reveal mechanisms for asymmetric and periodic protein binding to microtubules. We identify arc-MIPs, a novel class of microtubule inner protein, that bind laterally across protofilaments and remodel tubulin structure and lattice contacts. The binding mechanisms utilized by CA proteins may be generalizable to other microtubule-associated proteins. These structures establish a foundation to elucidate the contributions of individual CA proteins to ciliary motility and ciliopathies.

一对广泛修饰的微管形成大多数活动纤毛轴丝的中央装置 (CA)，它们在此处调节纤毛运动。两个 CA 微管的外表面均采用每隔 16 或 32 nm 重复一次的大型蛋白质复合物进行不对称图案化。这些投影的组成以及建立不对称性和纵向周期性的机制是未知的。在这里，通过确定 CA 微管的冷冻电镜结构，我们鉴定了 48 种不同的 CA 相关蛋白，这些蛋白反过来揭示了不对称和周期性蛋白质与微管结合的机制。我们确定了 arc-MIPs，一种新型的微管内部蛋白，它横向结合原丝并重塑微管蛋白结构和晶格接触。CA 蛋白使用的结合机制可以推广到其他微管相关蛋白。这些结构为阐明单个 CA 蛋白对纤毛运动和纤毛病的贡献奠定了基础。