EMD-32236

Single-particle
3.12 Å
EMD-32236 Deposition: 18/11/2021
Map released: 27/04/2022
Last modified: 26/06/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-32236

dmDicer2-LoqsPD-dsRNA Dimer status

EMD-32236

Single-particle
3.12 Å
EMD-32236 Deposition: 18/11/2021
Map released: 27/04/2022
Last modified: 26/06/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Drosophila melanogaster, Drosophila melanogaster, Spodoptera frugiperda
Sample: Dicer2-LoqsPD-dsRNA complex at its initial binding state
Fitted models: 7w0a (Avg. Q-score: 0.51)

Deposition Authors: Su S , Wang J
Structural insights into dsRNA processing by Drosophila Dicer-2-Loqs-PD.
Su S , Wang J , Deng T, Yuan X, He J , Liu N , Li X, Huang Y , Wang HW , Ma J
(2022) Nature , 607 , 399 - 406
PUBMED: 35768513
DOI: doi:10.1038/s41586-022-04911-x
ISSN: 1476-4687
ASTM: NATUAS
Abstract:
Small interfering RNAs (siRNAs) are the key components for RNA interference (RNAi), a conserved RNA-silencing mechanism in many eukaryotes1,2. 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)3,4. ATP hydrolysis by the helicase domain of Dcr-2 is critical to the successful processing of a long dsRNA into consecutive siRNA duplexes5,6. 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.