Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA

Metazoan microRNAs require specific maturation steps initiated by Microprocessor, comprising Drosha and DGCR8. Lack of structural information for the assembled complex has hindered an understanding of how Microprocessor recognizes primary microRNA transcripts (pri-miRNAs). Here we present a cryoelectron microscopy structure of human Microprocessor with a pri-miRNA docked in the active site, poised for cleavage. The basal junction is recognized by a four-way intramolecular junction in Drosha, triggered by the Belt and Wedge regions that clamp over the ssRNA. The belt is important for efficiency and accuracy of pri-miRNA processing. Two dsRBDs form a molecular ruler to measure the stem length between the two dsRNA-ssRNA junctions. The specific organization of the dsRBDs near the apical junction is independent of Drosha core domains, as observed in a second structure in the partially docked state. Collectively, we derive a molecular model to explain how Microprocessor recognizes a pri-miRNA and accurately identifies the cleavage site. [Display omitted] •Drosha and DGCR8 together form a “double-dsRBD ruler” to measure the stem length•Drosha Belt and Wedge clamp the ssRNA to ensure efficient and accurate processing•pri-miRNA GHG motif is recognized through the impact on the RNA structure via Wedge•HBRs and dsRBDs drive complex assembly with high affinity and intrinsic specificity Partin et al. present cryo-EM structures of the Microprocessor complex bound to a pri-miRNA, revealing how Drosha and DGCR8 recognize substrates and determine cleavage sites. Two dsRBDs form a molecular ruler to measure the stem length, and “Belt” and “Wedge” in Drosha play key roles in detecting the basal junction.