|Entry||Database: PDB / ID: 6bu9|
|Title||Drosophila Dicer-2 bound to blunt dsRNA|
|Keywords||rna binding protein/rna / Dicer / Dcr2 / Dcr-2 / dmDcr-2 / Dicer-2 / helicase / dsRNA / RNA / RNA BINDING PROTEIN / rna binding protein-rna complex|
|Function/homology||small RNA loading onto RISC / dsRNA transport / dosage compensation by hyperactivation of X chromosome / heterochromatin organization involved in chromatin silencing / Dicer double-stranded RNA-binding fold domain profile. / Dicer dimerisation domain / Dicer dimerisation domain / RNA interference / targeting of mRNA for destruction involved in RNA interference / deoxyribonuclease I activity ...small RNA loading onto RISC / dsRNA transport / dosage compensation by hyperactivation of X chromosome / heterochromatin organization involved in chromatin silencing / Dicer double-stranded RNA-binding fold domain profile. / Dicer dimerisation domain / Dicer dimerisation domain / RNA interference / targeting of mRNA for destruction involved in RNA interference / deoxyribonuclease I activity / ribonuclease III / adenosinetriphosphatase / siRNA loading onto RISC involved in RNA interference / Ribonuclease III family domain profile. / Ribonuclease III domain / detection of virus / Ribonuclease III domain / RISC-loading complex / Ribonuclease III, endonuclease domain superfamily / ribonuclease III activity / PAZ domain / PAZ domain profile. / production of siRNA involved in RNA interference / siRNA binding / RISC complex / PAZ domain / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / apoptotic DNA fragmentation / Double-stranded RNA binding motif / positive regulation of defense response to virus by host / chromatin silencing / mRNA cleavage / DEAD/DEAH box helicase domain / cellular response to virus / locomotory behavior / helicase activity / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / double-stranded RNA binding / Superfamilies 1 and 2 helicase C-terminal domain profile. / defense response to virus / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPase activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / nucleus / cytoplasm / Dicer-2, isoform A|
Function and homology information
|Specimen source||Drosophila melanogaster / arthropod / / |
|Method||Electron microscopy (6.8 Å resolution / Particle / Single particle) / Transmission electron microscopy|
|Authors||Shen, P.S. / Sinha, N.K. / Bass, B.L.|
|Citation||Journal: Science / Year: 2018|
Title: Dicer uses distinct modules for recognizing dsRNA termini.
Authors: Niladri K Sinha / Janet Iwasa / Peter S Shen / Brenda L Bass
Abstract: Invertebrates rely on Dicer to cleave viral double-stranded RNA (dsRNA), and Dicer-2 distinguishes dsRNA substrates by their termini. Blunt termini promote processive cleavage, while 3' overhanging ...Invertebrates rely on Dicer to cleave viral double-stranded RNA (dsRNA), and 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 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.
Copyright: 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
SummaryFull reportAbout validation report
|Date||Deposition: Dec 9, 2017 / Release: Dec 27, 2017|
Downloads & links
A: Dicer-2, isoform A
B: 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')
C: RNA (5'-R(*AP*CP*UP*AP*CP*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*C)-3')
|#1: Protein/peptide|| |
Mass: 198074.797 Da / Num. of mol.: 1
Source: (gene. exp.) Drosophila melanogaster / arthropod / /
Gene: Dcr-2, Dcr-2-RA, CG6493, Dmel_CG6493 / Production host: Spodoptera frugiperda
References: UniProt:A1ZAW0, EC:184.108.40.206 (ribonuclease III), EC:220.127.116.11 (adenosinetriphosphatase)
|#2: RNA chain|| |
Mass: 16781.023 Da / Num. of mol.: 1 / Source: (synth.) Unidentified
|#3: RNA chain|| |
Mass: 16528.768 Da / Num. of mol.: 1 / Source: (synth.) Unidentified
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Drosophila Dicer-2 bound to blunt dsRNA / Type: COMPLEX / Entity ID: 1,||Source (natural)||Organism: Drosophila melanogaster||Source (recombinant)||Organism: Spodoptera frugiperda||Buffer solution||pH: 8||Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES||Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
|Microscopy||Microscope model: FEI TECNAI 20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD|
|Image recording||Electron dose: 1.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 19445 / Symmetry type: POINT|
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