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- EMDB-7292: Drosophila Dicer-2 (apo, intact helicase density) -

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Basic information

Entry
Database: EMDB / ID: EMD-7292
TitleDrosophila Dicer-2 (apo, intact helicase density)
Map dataDrosophila Dicer-2 (intact helicase density)
Sample
  • Complex: Drosophila Dicer-2 (apo)
    • Protein or peptide: Dicer-2
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsShen PS / Sinha NK / Bass BL
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.
History
DepositionDec 9, 2017-
Header (metadata) releaseJan 10, 2018-
Map releaseJan 10, 2018-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7292.png

Downloads & links

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Map

FileDownload / File: emd_7292.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDrosophila Dicer-2 (intact helicase density)
Voxel sizeX=Y=Z: 1.193 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.0227887 - 0.03678357
Average (Standard dev.)0.000015886186 (±0.0013535204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 305.408 Å
α=β=γ: 90.0 °

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/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0230.0370.000

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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)
Components
  • Complex: Drosophila Dicer-2 (apo)
    • Protein or peptide: Dicer-2

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Supramolecule #1: Drosophila Dicer-2 (apo)

SupramoleculeName: Drosophila Dicer-2 (apo) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Dicer-2

MacromoleculeName: Dicer-2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPMEDVEIKP RGYQLRLVDH LTKSNGIVYL PTGSGKTFVA ILVLKRFSQD FDKPIESGGK RALFMCNTVE LARQQAMAVR RCTNFKVGFY VGEQGVDDWT RGMWSDEIKK NQVLVGTAQV FLDMVTQTYV ALSSLSVVII DECHHGTGHH PFREFMRLFT IANQTKLPRV ...String:
GPMEDVEIKP RGYQLRLVDH LTKSNGIVYL PTGSGKTFVA ILVLKRFSQD FDKPIESGGK RALFMCNTVE LARQQAMAVR RCTNFKVGFY VGEQGVDDWT RGMWSDEIKK NQVLVGTAQV FLDMVTQTYV ALSSLSVVII DECHHGTGHH PFREFMRLFT IANQTKLPRV VGLTGVLIKG NEITNVATKL KELEITYRGN IITVSDTKEM ENVMLYATKP TEVMVSFPHQ EQVLTVTRLI SAEIEKFYVS LDLMNIGVQP IRRSKSLQCL RDPSKKSFVK QLFNDFLYQM KEYGIYAASI AIISLIVEFD IKRRQAETLS VKLMHRTALT LCEKIRHLLV QKLQDMTYDD DDDNVNTEEV IMNFSTPKVQ RFLMSLKVSF ADKDPKDICC LVFVERRYTC KCIYGLLLNY IQSTPELRNV LTPQFMVGRN NISPDFESVL ERKWQKSAIQ QFRDGNANLM ICSSVLEEGI DVQACNHVFI LDPVKTFNMY VQSKGRARTT EAKFVLFTAD KEREKTIQQI YQYRKAHNDI AEYLKDRVLE KTEPELYEIK GHFQDDIDPF TNENGAVLLP NNALAILHRY CQTIPTDAFG FVIPWFHVLQ EDERDRIFGV SAKGKHVISI NMPVNCMLRD TIYSDPMDNV KTAKISAAFK ACKVLYSLGE LNERFVPKTL KERVASIADV HFEHWNKYGD SVTATVNKAD KSKDRTYKTE CPLEFYDALP RVGEICYAYE IFLEPQFESC EYTEHMYLNL QTPRNYAILL RNKLPRLAEM PLFSNQGKLH VRVANAPLEV IIQNSEQLEL LHQFHGMVFR DILKIWHPFF VLDRRSKENS YLVVPLILGA GEQKCFDWEL MTNFRRLPQS HGSNVQQREQ QPAPRPEDFE GKIVTQWYAN YDKPMLVTKV HRELTPLSYM EKNQQDKTYY EFTMSKYGNR IGDVVHKDKF MIEVRDLTEQ LTFYVHNRGK FNAKSKAKMK VILIPELCFN FNFPGDLWLK LIFLPSILNR MYFLLHAEAL RKRFNTYLNL HLLPFNGTDY MPRPLEIDYS LKRNVDPLGN VIPTEDIEEP KSLLEPMPTK SIEASVANLE ITEFENPWQK YMEPVDLSRN LLSTYPVELD YYYHFSVGNV CEMNEMDFED KEYWAKNQFH MPTGNIYGNR TPAKTNANVP ALMPSKPTVR GKVKPLLILQ KTVSKEHITP AEQGEFLAAI TASSAADVFD MERLEILGAS FLKLSATLYL ASKYSDWNEG TLTEVKSKLV SNRNLLFCLI DADIPKTLNT IQFTPRYTWL PPGISLPHNV LALWRENPEF AKIIGPHNLR DLALGDEESL VKGNCSDINY NRFVEGCRAN GQSFYAGADF SSEVNFCVGL VTIPNKVIAD TLEALLGVIV KNYGLQHAFK MLEYFKICRA DIDKPLTQLL NLELGGKKMR ANVNTTEIDG FLINHYYLEK NLGYTFKDRR YLLQALTHPS YPTNRITGSY QELEFIGAAI LDFLISAYIF ENNTKMNPGA LTDLRSALVN NTTLACICVR HRLHFFILAE NAKLSEIISK FVNFQESQGH RVTNYVRILL EEADVQPTPL DLDDELDMTE LPHANKCISQ EAEKGVPPKG EFNMSTNVDV PKALGDVLEA LIAAVYLDCR DLQRTWEVIF NLFEPELQEF TRKVPINHIR QLVEHKHAKP VFSSPIVEGE TVMVSCQFTC MEKTIKVYGF GSNKDQAKLS AAKHALQQLS KCDA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.2 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9730

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