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Structure paper

TitleStructural insights into dsRNA processing by Drosophila Dicer-2-Loqs-PD.
Journal, issue, pagesNature, Vol. 607, Issue 7918, Page 399-406, Year 2022
Publish dateJun 29, 2022
AuthorsShichen Su / Jia Wang / Ting Deng / Xun Yuan / Jinqiu He / Nan Liu / Xiaomin Li / Ying Huang / Hong-Wei Wang / Jinbiao Ma /
PubMed AbstractSmall 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 ...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.
External linksNature / PubMed:35768513 / PubMed Central
MethodsEM (single particle)
Resolution3.12 - 4.55 Å
Structure data

32236

7w0a

EMDB-32236, PDB-7w0a:
dmDicer2-LoqsPD-dsRNA Dimer status
Method: EM (single particle) / Resolution: 3.12 Å

32237

7w0b

EMDB-32237, PDB-7w0b:
Dicer2-LoqsPD complex at apo status
Method: EM (single particle) / Resolution: 3.33 Å

32238

7w0c

EMDB-32238, PDB-7w0c:
Dicer2-Loqs-PD-dsRNA complex at early-translocation state
Method: EM (single particle) / Resolution: 3.93 Å

32239

7w0d

EMDB-32239, PDB-7w0d:
Dicer2-LoqsPD-dsRNA complex at mid-translocation state
Method: EM (single particle) / Resolution: 4.18 Å

32240

7w0e

EMDB-32240, PDB-7w0e:
dmDicer2-LoqsPD-dsRNA Active-dicing status
Method: EM (single particle) / Resolution: 4.03 Å

32241

7w0f

EMDB-32241, PDB-7w0f:
dmDicer2-LoqsPD-dsRNA Post-dicing status
Method: EM (single particle) / Resolution: 4.55 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • drosophila melanogaster (fruit fly)
  • spodoptera frugiperda (fall armyworm)
KeywordsRNA BINDING PROTEIN / Ribonuclease

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