6BU9

Drosophila Dicer-2 bound to blunt dsRNA

• PDB DOI: https://doi.org/10.2210/pdb6BU9/pdb
• NAKB: 6BU9
• EM Map EMD-7290: EMDB EMDataResource

• Classification: rna binding protein/rna
• Organism(s): Drosophila melanogaster, unidentified
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-12-09 Released: 2017-12-27 
• Deposition Author(s): Shen, P.S., Sinha, N.K., Bass, B.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Dicer uses distinct modules for recognizing dsRNA termini.

Sinha, N.K., Iwasa, J., Shen, P.S., Bass, B.L.

(2018) Science 359: 329-334

• PubMed: 29269422 
• DOI: https://doi.org/10.1126/science.aaq0921
• Primary Citation of Related Structures:  
  6BU9, 6BUA


• PubMed Abstract: 
  

  Invertebrates rely on Dicer to cleave viral double-stranded RNA (dsRNA), and Drosophila Dicer-2 distinguishes dsRNA substrates by their termini. Blunt termini promote processive cleavage, while 3' overhanging termini are cleaved distributively. To understand this discrimination, we used cryo-electron microscopy to solve structures of Drosophila Dicer-2 alone and in complex with blunt dsRNA. Whereas the Platform-PAZ domains have been considered the only Dicer domains that bind dsRNA termini, unexpectedly, we found that the helicase domain is required for binding blunt, but not 3' overhanging, termini. We further showed that blunt dsRNA is locally unwound and threaded through the helicase domain in an adenosine triphosphate-dependent manner. Our studies reveal a previously unrecognized mechanism for optimizing antiviral defense and set the stage for the discovery of helicase-dependent functions in other Dicers.

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Organizational Affiliation: 

Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 231.38 kDa 
• Atom Count: 2,850 
• Modelled Residue Count: 440 
• Deposited Residue Count: 1,828 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dicer-2, isoform A	A	1,724	Drosophila melanogaster	Mutation(s): 0  Gene Names: Dcr-2, Dcr-2-RA, CG6493, Dmel_CG6493 EC: 3.1.26.3 (PDB Primary Data), 3.6.1.3 (PDB Primary Data)
UniProt
Find proteins for A1ZAW0 (Drosophila melanogaster) Explore A1ZAW0  Go to UniProtKB:  A1ZAW0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*AP*GP*U)-3')	B	52	unidentified

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*CP*UP*AP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*C)-3')	C	52	unidentified

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Shen, P.S., Sinha, N.K., Bass, B.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM121706

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2018-01-03
  Changes: Database references
• Version 1.2: 2018-01-17
  Changes: Author supporting evidence
• Version 1.3: 2018-01-31
  Changes: Database references
• Version 1.4: 2019-12-18
  Changes: Author supporting evidence, Other
• Version 1.5: 2024-03-13
  Changes: Data collection, Database references