|Entry||Database: EMDB / ID: 7291|
|Title||Drosophila Dicer-2 apo homology model (helicase, Platform-PAZ, RNaseIII domains)|
|Map data||Drosophila Dicer-2 (apo)|
|Sample||Drosophila Dicer-2 (apo):|
Dicer-2, isoform A
|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
|Source||Drosophila melanogaster (fruit fly)|
|Method||single particle reconstruction / cryo EM / 7.1 Å resolution|
|Authors||Shen PS / Sinha NK|
|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.
|Validation Report||PDB-ID: 6bua|
SummaryFull reportAbout validation report
|Date||Deposition: Dec 9, 2017 / Header (metadata) release: Dec 27, 2017 / Map release: Dec 27, 2017 / Last update: Jan 31, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_7291.map.gz (map file in CCP4 format, 67109 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.193 Å|
CCP4 map header:
-Entire Drosophila Dicer-2 (apo)
|Entire||Name: Drosophila Dicer-2 (apo) / Number of components: 2|
-Component #1: protein, Drosophila Dicer-2 (apo)
|Protein||Name: Drosophila Dicer-2 (apo) / Recombinant expression: No|
|Source||Species: Drosophila melanogaster (fruit fly)|
|Source (engineered)||Expression System: Spodoptera frugiperda (fall armyworm)|
-Component #2: protein, Dicer-2, isoform A
|Protein||Name: Dicer-2, isoform A / Recombinant expression: No|
|Mass||Theoretical: 198.074797 kDa|
|Source (engineered)||Expression System: Drosophila melanogaster (fruit fly)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 8|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.2 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 85119|
|3D reconstruction||Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF|
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