7W0D

Dicer2-LoqsPD-dsRNA complex at mid-translocation state

Summary for 7W0D

• Entry DOI: 10.2210/pdb7w0d/pdb
• EMDB information: 32239
• Descriptor: Loquacious, isoform D, dsRNA, Dicer-2, isoform A, ... (5 entities in total)
• Functional Keywords: ribonuclease, rna binding protein
• Biological source: Drosophila melanogaster (Fruit fly); More
• Total number of polymer chains: 6
• Total formula weight: 507215.28

Authors

Su, S.,Wang, J.,Wang, H.W.,Ma, J. (deposition date: 2021-11-18, release date: 2022-04-27, Last modification date: 2024-06-26)

Primary citation

Su, S.,Wang, J.,Deng, T.,Yuan, X.,He, J.,Liu, N.,Li, X.,Huang, Y.,Wang, H.W.,Ma, J.
Structural insights into dsRNA processing by Drosophila Dicer-2-Loqs-PD.
Nature, 607:399-406, 2022

PubMed Abstract: Small interfering RNAs (siRNAs) are the key components for RNA interference (RNAi), a conserved RNA-silencing mechanism in many eukaryotes. In Drosophila, an RNase III enzyme Dicer-2 (Dcr-2), aided by its cofactor Loquacious-PD (Loqs-PD), has an important role in generating 21 bp siRNA duplexes from long double-stranded RNAs (dsRNAs). ATP hydrolysis by the helicase domain of Dcr-2 is critical to the successful processing of a long dsRNA into consecutive siRNA duplexes. Here we report the cryo-electron microscopy structures of Dcr-2-Loqs-PD in the apo state and in multiple states in which it is processing a 50 bp dsRNA substrate. The structures elucidated interactions between Dcr-2 and Loqs-PD, and substantial conformational changes of Dcr-2 during a dsRNA-processing cycle. The N-terminal helicase and domain of unknown function 283 (DUF283) domains undergo conformational changes after initial dsRNA binding, forming an ATP-binding pocket and a 5'-phosphate-binding pocket. The overall conformation of Dcr-2-Loqs-PD is relatively rigid during translocating along the dsRNA in the presence of ATP, whereas the interactions between the DUF283 and RIIIDb domains prevent non-specific cleavage during translocation by blocking the access of dsRNA to the RNase active centre. Additional ATP-dependent conformational changes are required to form an active dicing state and precisely cleave the dsRNA into a 21 bp siRNA duplex as confirmed by the structure in the post-dicing state. Collectively, this study revealed the molecular mechanism for the full cycle of ATP-dependent dsRNA processing by Dcr-2-Loqs-PD.

PubMed: 35768513
DOI: 10.1038/s41586-022-04911-x

Experimental method

ELECTRON MICROSCOPY (4.18 Å)