IFT-A structure reveals carriages for membrane protein transport into cilia

Intraflagellar transport (IFT) trains are massive molecular machines that traffic proteins between cilia and the cell body. Each IFT train is a dynamic polymer of two large complexes (IFT-A and -B) and motor proteins, posing a formidable challenge to mechanistic understanding. Here, we reconstituted the complete human IFT-A complex and obtained its structure using cryo-EM. Combined with AlphaFold prediction and genome-editing studies, our results illuminate how IFT-A polymerizes, interacts with IFT-B, and uses an array of β-propeller and TPR domains to create “carriages” of the IFT train that engage TULP adaptor proteins. We show that IFT-A⋅TULP carriages are essential for cilia localization of diverse membrane proteins, as well as ICK—the key kinase regulating IFT train turnaround. These data establish a structural link between IFT-A’s distinct functions, provide a blueprint for IFT-A in the train, and shed light on how IFT evolved from a proto-coatomer ancestor. [Display omitted] •Cryo-EM structure of intraflagellar transport complex A (IFT-A)•IFT-A is built around a dimer-of-dimers that evolved from a proto-coatomer ancestor•IFT-A polymerization creates carriages next to ciliary membrane•Carriages localize diverse membrane proteins and key kinase for IFT train turnaround A high-resolution structure of the human intraflagellar transport complex A unveils the ways in which the complex is assembled into intraflagellar transport trains, facilitates cargo transport, and regulates train movement in cilia and flagella.