Structure and tethering mechanism of dynein-2 intermediate chains in intraflagellar transport

Dynein-2 is a large multiprotein complex that powers retrograde intraflagellar transport (IFT) of cargoes within cilia/flagella, but the molecular mechanism underlying this function is still emerging. Distinctively, dynein-2 contains two identical force-generating heavy chains that interact with two different intermediate chains (WDR34 and WDR60). Here, we dissect regulation of dynein-2 function by WDR34 and WDR60 using an integrative approach including cryo-electron microscopy and CRISPR/Cas9-enabled cell biology. A 3.9 Å resolution structure shows how WDR34 and WDR60 use surprisingly different interactions to engage equivalent sites of the two heavy chains. We show that cilia can assemble in the absence of either WDR34 or WDR60 individually, but not both subunits. Dynein-2-dependent distribution of cargoes depends more strongly on WDR60, because the unique N-terminal extension of WDR60 facilitates dynein-2 targeting to cilia. Strikingly, this N-terminal extension can be transplanted onto WDR34 and retain function, suggesting it acts as a flexible tether to the IFT “trains” that assemble at the ciliary base. We discuss how use of unstructured tethers represents an emerging theme in IFT train interactions. Synopsis Dynein-2 is the molecular motor responsible for intraflagellar transport (IFT) from the tip of cilia to the base. Here, a combination of cryo-electron microscopy, crystallography, genome editing, and live-cell imaging defines the contribution of heterodimeric intermediate chains (WDR34 and WDR60) to dynein-2 cellular function. WDR34 and WDR60 use distinct interactions to engage equivalent sites of the two dynein-2 motor subunits. Cilia can assemble in the absence of either WDR34 or WDR60, but not when both subunits are missing. Dynein-2 function depends more strongly on WDR60, whose unique N-terminal extension facilitates dynein-2 targeting to cilia. This N-terminal extension can be transplanted onto WDR34 and retain function, suggesting it acts as a flexible tether to IFT complexes assembling at the ciliary base. The N-terminal extension of dynein-2 intermediate chain WDR60 tethers dynein-2 to intraflagellar transport complexes in cilia.