8DFV | pdb_00008dfv

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

• PDB DOI: https://doi.org/10.2210/pdb8DFV/pdb
• EM Map EMD-27415: EMDB EMDataResource
• NAKB: 8DFV

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Drosophila melanogaster
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2022-06-22 Released: 2022-11-16 
• Deposition Author(s): Jouravleva, K., Golovenko, D., Demo, G., Dutcher, R.C., Tanaka Hall, T.M., Zamore, P.D., Korostelev, A.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: 2D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 36182693 
• DOI: https://doi.org/10.1016/j.molcel.2022.09.002
• Primary Citation 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.

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Organizational Affiliation: 
• RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 62500, Czech Republic.
Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA. Electronic address: [e-mail].
RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Electronic address: [e-mail].
RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 325.39 kDa 
• Atom Count: 16,710 
• Modeled Residue Count: 1,977 
• Deposited Residue Count: 2,774 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease Dcr-1	A	2,249	Drosophila melanogaster	Mutation(s): 0  Gene Names: Dcr-1, CG4792 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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Loquacious, isoform B	C [auth K]	465	Drosophila melanogaster	Mutation(s): 0  Gene Names: CG6866
UniProt
Find proteins for Q9VJY9 (Drosophila melanogaster) Explore Q9VJY9  Go to UniProtKB:  Q9VJY9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (60-MER)	B [auth E]	60	Drosophila melanogaster

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth A], F [auth A], G [auth A], H [auth E], I [auth E], J [auth E], K [auth E], L [auth E], M [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: 2D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Jouravleva, K., Golovenko, D., Demo, G., Dutcher, R.C., Tanaka Hall, T.M., Zamore, P.D., Korostelev, A.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM136275
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM127094
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1ZIA50165

Revision History  

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