7VG2

Cryo-EM structure of Arabidopsis DCL3 in complex with a 40-bp RNA

Summary for 7VG2

• Entry DOI: 10.2210/pdb7vg2/pdb
• EMDB information: 31963
• Descriptor: Dicer-like 3, TAS1a forward strand (5'-phosphorylation), TAS1a reverse strand, ... (5 entities in total)
• Functional Keywords: dcl3, rna, rddm, dicer, rna binding protein, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Arabidopsis thaliana (Mouse-ear cress); More
• Total number of polymer chains: 3
• Total formula weight: 208177.70

Authors

Wang, Q.,Du, J. (deposition date: 2021-09-14, release date: 2021-10-27, Last modification date: 2024-06-19)

Primary citation

Wang, Q.,Xue, Y.,Zhang, L.,Zhong, Z.,Feng, S.,Wang, C.,Xiao, L.,Yang, Z.,Harris, C.J.,Wu, Z.,Zhai, J.,Yang, M.,Li, S.,Jacobsen, S.E.,Du, J.
Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation.
Science, 374:1152-1157, 2021

PubMed Abstract: In eukaryotes, small RNAs (sRNAs) play critical roles in multiple biological processes. Dicer endonucleases are a central part of sRNA biogenesis. In plants, DICER-LIKE PROTEIN 3 (DCL3) produces 24-nucleotide (nt) small interfering RNAs (siRNAs) that determine the specificity of the RNA-directed DNA methylation pathway. Here, we determined the structure of a DCL3–pre-siRNA complex in an active dicing-competent state. The 5′-phosphorylated A1 of the guide strand and the 1-nt 3′ overhang of the complementary strand are specifically recognized by a positively charged pocket and an aromatic cap, respectively. The 24-nt siRNA length dependence relies on the separation between the 5′-phosphorylated end of the guide RNA and dual cleavage sites formed by the paired ribonuclease III domains. These structural studies, complemented by functional data, provide insight into the dicing principle for Dicers in general.

PubMed: 34648373
DOI: 10.1126/science.abl4546

Experimental method

ELECTRON MICROSCOPY (3.1 Å)