7ELD | pdb_00007eld

Cryo-EM structure of Arabidopsis DCL1 in complex with pri-miRNA 166f


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7ELD

This is version 1.2 of the entry. See complete history

Literature

Structural basis of microRNA processing by Dicer-like 1.

Wei, X.Ke, H.Wen, A.Gao, B.Shi, J.Feng, Y.

(2021) Nat Plants 7: 1389-1396

  • DOI: https://doi.org/10.1038/s41477-021-01000-1
  • Primary Citation Related Structures: 
    7ELD, 7ELE

  • PubMed Abstract: 

    MicroRNAs (miRNAs) are short non-coding RNAs that inhibit the expression of target genes by directly binding to their mRNAs. In animals, pri-miRNAs are cleaved by Drosha to generate pre-miRNAs, which are subsequently cleaved by Dicer to generate mature miRNAs. Instead of being cleaved by two different enzymes, both cleavages in plants are performed by Dicer-like 1 (DCL1). With a similar domain architecture as human Dicer, it is mysterious how DCL1 recognizes pri-miRNAs and performs two cleavages sequentially. Here, we report the single-particle cryo-electron microscopy structures of Arabidopsis DCL1 complexed with a pri-miRNA and a pre-miRNA, respectively, in cleavage-competent states. These structures uncover the plasticity of the PAZ domain, which is critical for the recognition of both pri-miRNA and pre-miRNA. These structures suggest that the helicase module serves as an engine that transfers the substrate between two sequential cleavage events. This study lays a foundation for dissecting the regulation mechanism of miRNA biogenesis in plants and provides insights into the dicing state of human Dicer.


  • Organizational Affiliation
    • Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 261.06 kDa 
  • Atom Count: 11,282 
  • Modeled Residue Count: 1,246 
  • Deposited Residue Count: 2,057 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endoribonuclease Dicer homolog 11,909Arabidopsis thalianaMutation(s): 0 
Gene Names: DCL1ASU1CAF SIN1SUS1At1g01040T25K16.4
EC: 3.1.26
UniProt
Find proteins for Q9SP32 (Arabidopsis thaliana)
Explore Q9SP32 
Go to UniProtKB:  Q9SP32
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SP32
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
pri-miRNA 166f148Arabidopsis thaliana
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31970040

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2024-06-05
    Changes: Data collection