8DG7

Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB - complex III


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 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

Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB.

Jouravleva, K.Golovenko, D.Demo, G.Dutcher, R.C.Hall, T.M.T.Zamore, P.D.Korostelev, A.A.

(2022) Mol Cell 82: 4049-4063.e6

  • DOI: https://doi.org/10.1016/j.molcel.2022.09.002
  • Primary Citation of Related Structures:  
    8DFV, 8DG5, 8DG7, 8DGA, 8DGI, 8DGJ

  • PubMed Abstract: 

    In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 that show how Dicer-1 and its partner Loqs‑PB cooperate (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, and (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicer‑1⋅Loqs‑PB heterodimer. The Dicer-1 dsRBD and three Loqs‑PB dsRBDs form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-miRNA cleavage shifts the dsRBDs and partially closes Dicer-1, which may promote product release. Our data suggest a model for how the Dicer‑1⋅Loqs‑PB complex affects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and product release.


  • Organizational Affiliation

    RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoribonuclease Dcr-12,249Drosophila melanogasterMutation(s): 0 
Gene Names: Dcr-1CG4792
EC: 3.1.26 (PDB Primary Data), 3.1.26.3 (UniProt)
UniProt
Find proteins for Q9VCU9 (Drosophila melanogaster)
Explore Q9VCU9 
Go to UniProtKB:  Q9VCU9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VCU9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Loquacious, isoform BD [auth K]465Drosophila melanogasterMutation(s): 0 
Gene Names: CG6866
UniProt
Find proteins for Q9VJY9 (Drosophila melanogaster)
Explore Q9VJY9 
Go to UniProtKB:  Q9VJY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VJY9
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (22-MER)B [auth E]21Drosophila melanogaster
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (38-MER)C [auth F]38Drosophila melanogaster
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U5P
Query on U5P

Download Ideal Coordinates CCD File 
I [auth E]URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
J [auth E]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth E],
K [auth E],
L [auth E],
M [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM136275
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM127094
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIA50165

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Data collection