Cilia and flagella are highly conserved motile and sensory organelles in eukaryotes, and defects in ciliary assembly and motility cause many ciliopathies. The two-headed I1 inner arm dynein is a critical regulator of ciliary and flagellar beating. To understand I1 architecture and function better, we analyzed the 3D structure and composition of the I1 dynein in Chlamydomonas axonemes by cryoelectron tomography and subtomogram averaging. Our data revealed several connections from the I1 dynein to neighboring structures that are likely to be important for assembly and/or regulation, including a tether linking one I1 motor domain to the doublet microtubule and doublet-specific differences potentially contributing to the asymmetrical distribution of dynein activity required for ciliary beating. We also imaged three I1 mutants and analyzed their polypeptide composition using 2D gel-based proteomics. Structural and biochemical comparisons revealed the likely location of the regulatory IC138 phosphoprotein and its associated subcomplex. Overall, our studies demonstrate that I1 dynein is connected to multiple structures within the axoneme, and therefore ideally positioned to integrate signals that regulate ciliary motility.dynein f | flagella C ilia and flagella are highly conserved organelles with roles in cellular movement and signal transduction. In humans, defects in cilia can lead to a number of diseases, such as polycystic kidney disease and primary ciliary dyskinesia (1, 2). The axoneme core of most motile cilia and flagella consists of nine doublet microtubules (DMTs) surrounding two single microtubules (MTs) known as the central pair complex (CPC) (Fig. 1). DMTs are highly periodic with a 96-nm-long unit that repeats along the MT length. They are decorated with two rows of dynein motors, the inner dynein arms (IDAs) and the outer dynein arms (ODAs), which drive MT sliding and axoneme bending (3). Generating the diverse ciliary and flagellar waveforms requires the precise coordination of the activity of thousands of dynein motors within a single organelle (4).The primary signaling pathway known to regulate dynein function in axonemes involves signals traveling from the CPC through radial spokes (RSs) to the IDAs and ODAs (reviewed in 5, 6). Many CPC and RS mutants are paralyzed (7). However, MT sliding can be restored to WT levels in isolated CPC/RS mutant axonemes using protein kinase inhibitors (8, 9). These observations, together with biochemical evidence of phosphorylation of dynein subunits, have implicated the dyneins as a major signaling target of the CPC/RS signaling pathway (10, 11). However, the regulatory mechanisms and physical interactions that participate in signal transduction to the dynein targets are not well understood.Isolated axonemes require only ATP for reactivation, suggesting that direct interactions between the dyneins and their regulators are physically built into the axoneme (4). Therefore, studies that visualize axonemal structures and their connections at high resolution can provide ...