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- EMDB-7291: Drosophila Dicer-2 apo homology model (helicase, Platform-PAZ, RN... -

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Basic information

Entry
Database: EMDB / ID: 7291
TitleDrosophila Dicer-2 apo homology model (helicase, Platform-PAZ, RNaseIII domains)
Map dataDrosophila Dicer-2 (apo)
SampleDrosophila Dicer-2 (apo):
Dicer-2, isoform A
Function / homologyHelicase, 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 / siRNA loading onto RISC involved in RNA interference / adenosinetriphosphatase / detection of virus / RISC-loading complex / production of siRNA involved in RNA interference / ribonuclease III activity / siRNA binding / RISC complex / 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
SourceDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / 7.1 Å resolution
AuthorsShen PS / Sinha NK
CitationJournal: 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 ReportPDB-ID: 6bua

SummaryFull reportAbout validation report
DateDeposition: Dec 9, 2017 / Header (metadata) release: Dec 27, 2017 / Map release: Dec 27, 2017 / Last update: Jan 31, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6bua
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7291.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.19 Å/pix.
= 305.408 Å
256 pix
1.19 Å/pix.
= 305.408 Å
256 pix
1.19 Å/pix.
= 305.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.193 Å
Density
Contour Level:0.013 (by author), 0.013 (movie #1):
Minimum - Maximum-0.0038245027 - 0.030697713
Average (Standard dev.)-3.1299314E-5 (0.0012950517)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 305.408 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1931.1931.193
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z305.408305.408305.408
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0040.031-0.000

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Supplemental data

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Sample components

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Entire Drosophila Dicer-2 (apo)

EntireName: Drosophila Dicer-2 (apo) / Number of components: 2

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Component #1: protein, Drosophila Dicer-2 (apo)

ProteinName: Drosophila Dicer-2 (apo) / Recombinant expression: No
SourceSpecies: Drosophila melanogaster (fruit fly)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, Dicer-2, isoform A

ProteinName: Dicer-2, isoform A / Recombinant expression: No
MassTheoretical: 198.074797 kDa
Source (engineered)Expression System: Drosophila melanogaster (fruit fly)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 85119
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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