|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||Helicase, C-terminal / Helicase conserved C-terminal domain / Helicase superfamily 1/2, ATP-binding domain / Double-stranded RNA-binding domain / P-loop containing nucleoside triphosphate hydrolase / Ribonuclease III, endonuclease domain superfamily / Dicer dimerisation domain superfamily / Double-stranded RNA binding motif / Ribonuclease III domain / DEAD/DEAH box helicase ...Helicase, C-terminal / Helicase conserved C-terminal domain / Helicase superfamily 1/2, ATP-binding domain / Double-stranded RNA-binding domain / P-loop containing nucleoside triphosphate hydrolase / Ribonuclease III, endonuclease domain superfamily / Dicer dimerisation domain superfamily / Double-stranded RNA binding motif / Ribonuclease III domain / DEAD/DEAH box helicase / Dicer dimerisation domain / DEAD/DEAH box helicase domain / Ribonuclease III domain / PAZ domain / Dicer dimerisation domain / Double stranded RNA-binding domain (dsRBD) profile. / Ribonuclease III family domain profile. / PAZ domain / PAZ domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Dicer double-stranded RNA-binding fold domain profile. / bidentate ribonuclease III activity / small RNA loading onto RISC / dsRNA transport / dosage compensation by hyperactivation of X chromosome / heterochromatin organization involved in chromatin silencing / 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 / detection of virus / RISC-loading complex / production of siRNA involved in RNA interference / ribonuclease III activity / RISC complex / siRNA binding / RNA phosphodiester bond hydrolysis, endonucleolytic / apoptotic DNA fragmentation / positive regulation of defense response to virus by host / chromatin silencing / cellular response to virus / locomotory behavior / helicase activity / double-stranded RNA binding / defense response to virus / ATPase activity / ATP binding / nucleus / cytoplasm / Dicer-2, isoform A|
Function and homology information
|Specimen source||Drosophila melanogaster (fruit fly)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.8 Å resolution|
|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.
SummaryFull reportAbout validation report
|Date||Deposition: Dec 9, 2017 / Release: Dec 27, 2017|
|Structure viewer||Molecule: |
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 (fruit fly) / Gene: Dcr-2, Dcr-2-RA, CG6493, Dmel_CG6493 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A1ZAW0, ribonuclease III, adenosinetriphosphatase
|#2: RNA chain|| |
Mass: 16781.023 Da / Num. of mol.: 1 / Source: (synth.) unidentified (others)
|#3: RNA chain|| |
Mass: 16528.768 Da / Num. of mol.: 1 / Source: (synth.) unidentified (others)
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: Drosophila Dicer-2 bound to blunt dsRNA / Type: COMPLEX / Entity ID: 1,||Source (natural)||Organism: Drosophila melanogaster (fruit fly)||Source (recombinant)||Organism: Spodoptera frugiperda (fall armyworm)||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 FIELDBright-field microscopy|
|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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