The microtubules composing each doublet are constructed so that the wall of one microtubule, designated the B micro-tubule, is actually incomplete; it shares a portion of the wall of the other microtubule of the doublet, the A microtubule. The A microtubule is composed of 13 tubulin protoflaments, arranged in side-by-side configuration, whereas the B micro-tubule is composed of 10 tubulin protoflaments. Tubulin molecules incorporated into ciliary microtubules are tightly bound together and post-translationally modified in the process of acetylation and polyglutamylation. Such modifications ensure that microtubules of ciliary axoneme are highly stable and resist depolymerization.
When seen in cross-section at high resolution, each doublet exhibits a pair of “arms” that contain ciliary dynein, a microtubule-associated motor protein. This motor protein uses the energy of adenosine triphosphate (ATP) hydrolysis to move along the surface of the adjacent microtubule (see Fig. 5.7). The dynein arms occur at 24-nm intervals along the length of the A microtubule and extend out to form temporary cross-bridges with the B microtubule of the adjacent doublet. A passive elastic component formed by nexin (165 kilodaltons) permanently links the A microtubule with the B microtubule of adjacent doublets at 86-nm intervals. The two central microtubules are separate but partially enclosed by a central sheath projection at 14-nm intervals along the length of the cilium (see Fig. 5.7). Radial spokes extend from each of the nine doublets toward the two central microtubules at 29-nm intervals. The proteins forming the radial spokes and the nexin connections between the outer doublets make large-amplitude oscillations of the cilia possible.
Basal bodies and basal body–associated structures firmly anchor cilia in the apical cell cytoplasm.
The 9  2 microtubule array courses from the tip of the cilium to its base, whereas the outer paired microtubules join the basal body. The basal body is a modified centriole. It functions as an MTOC consisting of nine short microtubule triplets arranged in a ring. Each of the paired microtubules of the ciliary axoneme (A and B microtubules) is continuous with two of the triplet microtubules of the basal body. The third incomplete C microtubule in the triplet extends from the bottom to the transitional zone at the top of the basal body near the transition between the basal body and the axoneme. The two central micro-tubules of the cilium originate at the transitional zone and extend to the top of axoneme (see Fig. 5.7b). Therefore, a cross-section of the basal body would reveal nine circularly arranged microtubule triplets but not the two central single microtubules of the cilium.
Basal bodies are associated with several basal body– associated structures such as alar sheets (transitional fibers), basal feet, and striated rootlets (see Fig. 5.7 and Fig 5.8).  The alar sheet (transitional fiber) is a collarlike extension between the transitional zone of basal body and plasma membrane. It originates near the top end of the basal body
C microtubule and inserts into the cytoplasmic domain of the plasma membrane. It tethers the basal body to the apical plasma membrane (see Fig 5.7).