7XW3

Cryo-EM structure of an apo-form of human DICER


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.04 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the human DICER-pre-miRNA complex in a dicing state.

Lee, Y.Y.Lee, H.Kim, H.Kim, V.N.Roh, S.H.

(2023) Nature 615: 331-338

  • DOI: https://doi.org/10.1038/s41586-023-05723-3
  • Primary Citation of Related Structures:  
    7XW2, 7XW3

  • PubMed Abstract: 

    Dicer has a key role in small RNA biogenesis, processing double-stranded RNAs (dsRNAs) 1,2 . Human DICER (hDICER, also known as DICER1) is specialized for cleaving small hairpin structures such as precursor microRNAs (pre-miRNAs) and has limited activity towards long dsRNAs-unlike its homologues in lower eukaryotes and plants, which cleave long dsRNAs. Although the mechanism by which long dsRNAs are cleaved has been well documented, our understanding of pre-miRNA processing is incomplete because structures of hDICER in a catalytic state are lacking. Here we report the cryo-electron microscopy structure of hDICER bound to pre-miRNA in a dicing state and uncover the structural basis of pre-miRNA processing. hDICER undergoes large conformational changes to attain the active state. The helicase domain becomes flexible, which allows the binding of pre-miRNA to the catalytic valley. The double-stranded RNA-binding domain relocates and anchors pre-miRNA in a specific position through both sequence-independent and sequence-specific recognition of the newly identified 'GYM motif' 3 . The DICER-specific PAZ helix is also reoriented to accommodate the RNA. Furthermore, our structure identifies a configuration of the 5' end of pre-miRNA inserted into a basic pocket. In this pocket, a group of arginine residues recognize the 5' terminal base (disfavouring guanine) and terminal monophosphate; this explains the specificity of hDICER and how it determines the cleavage site. We identify cancer-associated mutations in the 5' pocket residues that impair miRNA biogenesis. Our study reveals how hDICER recognizes pre-miRNAs with stringent specificity and enables a mechanistic understanding of hDICER-related diseases.


  • Organizational Affiliation

    Center for RNA Research, Institute for Basic Science (IBS), Seoul, Republic of Korea. narrykim@snu.ac.kr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoribonuclease Dicer1,922Homo sapiensMutation(s): 0 
Gene Names: DICER1DICERHERNAKIAA0928
EC: 3.1.26.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPY3 (Homo sapiens)
Explore Q9UPY3 
Go to UniProtKB:  Q9UPY3
GTEx:  ENSG00000100697 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UPY3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.04 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references