Cilia are made primarily of protein, specifically repeating units of a protein called tubulin that assemble into hollow tubes known as microtubules. These microtubules form the internal skeleton of every cilium, and hundreds of additional proteins attach to this framework to give cilia their structure, movement capability, and sensory functions. A single cilium contains an estimated 700 or more distinct proteins, all wrapped in a specialized extension of the cell membrane.
The Tubulin Backbone
The core of every cilium is a structure called the axoneme, which runs the full length of the cilium like an internal scaffold. The axoneme is built from microtubules, and each microtubule is assembled from two forms of a protein called tubulin (alpha and beta). These two tubulin molecules lock together in pairs, then stack end to end like bricks in a column to form long filaments called protofilaments. Thirteen protofilaments curve around to form one complete tube.
In motile cilia (the kind that beat back and forth to move fluid), nine pairs of microtubules are arranged in a ring around two single microtubules in the center. This pattern is called the 9+2 arrangement. Each outer pair is actually a “doublet” with one complete tube of 13 protofilaments (the A tubule) fused to an incomplete tube of 10 protofilaments (the B tubule). The two central microtubules are full, standalone tubes. This architecture is remarkably consistent across species, from single-celled algae to human airways.
Primary cilia, which act as sensory antennae on most cells in the body, have a slightly different layout. They keep the nine outer doublets but lack the two central microtubules entirely, giving them a 9+0 arrangement. This missing center pair is one reason primary cilia generally don’t move. A third variation exists in nodal cilia, which appear during embryonic development. These also have a 9+0 structure but can rotate in a way that helps establish left-right body symmetry.
Motor Proteins That Power Movement
Tubulin alone would give you a rigid stick, not a beating cilium. Movement comes from motor proteins called dyneins, which are attached along the outer doublet microtubules in two rows: outer dynein arms and inner dynein arms. Dynein works by grabbing onto a neighboring microtubule doublet and pulling on it, causing the doublets to slide against each other. Because the doublets are anchored at the base, this sliding force bends the cilium instead of pulling it apart.
The bending has to be coordinated, though, or the cilium would just twitch randomly. That coordination depends on two other protein structures. Radial spokes are T-shaped protein complexes that extend inward from each doublet toward the central pair of microtubules. They transmit regulatory signals from the central pair outward, telling the dynein motors when to activate. The nexin-dynein regulatory complex (often called N-DRC) connects neighboring doublets to each other and acts as the main coordination hub. It receives signals from the radial spokes and adjusts dynein activity accordingly, while also holding the entire axoneme together so the doublets don’t fly apart during movement.
When any of these protein components are defective, ciliary movement breaks down. Mutations in genes encoding outer dynein arm proteins, radial spoke head proteins, or nexin-regulatory complex components all cause primary ciliary dyskinesia, a condition where cilia beat weakly or abnormally. This leads to chronic respiratory infections, because the cilia lining the airways can’t clear mucus properly.
The Basal Body Anchor
Every cilium grows from a structure embedded in the cell called the basal body, which is made of the same tubulin proteins but arranged differently. Instead of nine doublets, the basal body has nine triplets: three fused microtubules per blade instead of two. These triplets span about 400 nanometers in length. At the top of the basal body, the C tubule (the outermost of the three) drops off, leaving just the A and B tubules to continue upward as the doublets of the axoneme.
The basal body also contains non-tubulin proteins that form a large inner scaffold running through its hollow center, stabilizing the entire barrel shape. A transition zone sits between the basal body and the axoneme proper, acting as a gatekeeper that controls which proteins are allowed into the cilium. This selectivity is part of what makes the cilium a distinct compartment with its own unique protein and lipid composition.
How Cilia Build Themselves
Cilia can’t manufacture their own proteins because they don’t contain ribosomes (the cell’s protein-making machinery). Every component has to be built in the main cell body and then transported to the tip of the growing cilium, where new material is added. This delivery system is called intraflagellar transport, or IFT.
IFT relies on multi-protein complexes that work like cargo trains. Two sub-complexes, called IFT-A and IFT-B, together contain at least 15 protein subunits that act as adapters between motor proteins (which provide the movement along the microtubule tracks) and the cargo being delivered. IFT-B is responsible for outward transport toward the tip, and when it’s defective, cilia either fail to form or are dramatically shortened. IFT-A handles return transport back to the base, and mutations in IFT-A proteins produce misshapen cilia with bulging accumulations of stranded cargo.
The Ciliary Membrane
Surrounding the entire axoneme is a membrane that is continuous with, but chemically distinct from, the rest of the cell’s outer membrane. The ciliary membrane is enriched in sterols, sphingolipids, and glycolipids, a combination associated with lipid raft microdomains that help organize signaling receptors. This specialized lipid mix makes the ciliary membrane stiffer and more organized than the general cell membrane.
Embedded in this membrane are receptor proteins that allow cilia to detect signals from outside the cell. In the eye, photoreceptor cells use a modified cilium packed with the light-sensing protein rhodopsin. In the kidneys, cilia on tubule cells carry polycystin-2, a channel protein involved in sensing fluid flow. Olfactory neurons have cilia loaded with cyclic-nucleotide-gated channels that translate chemical signals into nerve impulses. Each cell type loads its cilia with different membrane proteins depending on what the cilia need to sense.
Total Protein Count
Recent spatial proteomics work has begun mapping the full inventory of ciliary proteins. One large-scale study using antibody-based imaging across three human cell lines tested nearly 2,000 candidate proteins and confirmed 715 of them localizing to different regions of primary cilia, including the tip, transition zone, and basal body. The true total is likely higher, since many proteins are present in low amounts or only in specific cell types. This complexity reflects the fact that cilia are not simple cellular hairs but highly organized structures where precise protein composition determines whether the cilium beats, senses light, detects chemicals, or responds to developmental signals.