7VG2

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation.

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.

(2021) Science 374: 1152-1157

  • DOI: https://doi.org/10.1126/science.abl4546
  • Primary Citation of Related Structures:  
    7VG2, 7VG3

  • 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.


  • Organizational Affiliation

    Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dicer-like 31,621Arabidopsis thalianaMutation(s): 0 
Gene Names: DCL3ATDCL3DICER-LIKE 3At3g43920
UniProt
Find proteins for Q9LXW7 (Arabidopsis thaliana)
Explore Q9LXW7 
Go to UniProtKB:  Q9LXW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LXW7
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
TAS1a forward strand (5'-phosphorylation)B [auth C]40Arabidopsis thaliana
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
TAS1a reverse strandC [auth D]41Arabidopsis thaliana
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references