DNAHX: a novel, non-motile dynein heavy chain subfamily, identified by cryo-EM endogenously.

Ciliogenesis and cilia motility rely on the coordinated actions of diverse dyneins, yet the complexity of these motor proteins in cilia has posed challenges for understanding their specific roles. Traditional evolutionary analyses often overlook key family members due to technical limitations. Here, we present a cryo-EM-based, bottom-up approach for large-scale, protein identification and functional prediction of endogenous axonemal dynein complexes. This approach led to the identification of a novel dynein heavy chain subfamily (XP_041462850), designated as DNAHX, from sea urchin sperm. Phylogenetic analysis indicates that DNAHX branches from the outer-arm dynein alpha chain during evolution and is found in specific animal lineages with external fertilization. DNAHX contains multiple insertions throughout the protein, locking DNAHX permanently in a pre-powerstroke state. The AAA1 site exhibits poor conservation of essential ATPase motifs, consistent with DNAHX's non-motile nature. DNAHX also forms a heterodimeric dynein complex, which we named dynein-X, with another dynein heavy chain and accessory chains. Furthermore, a subset of dynein-X displays an autoinhibited phi particle conformation, potentially facilitating the intraflagellar transport of axonemal dyneins. Our discovery of the novel, non-motile dynein heavy chain and the dynein-X complex provides valuable insights into the evolution of dyneins and potentially their diverse cellular functions.