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- PDB-6bua: Drosophila Dicer-2 apo homology model (helicase, Platform-PAZ, RN... -

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Basic information

Entry
Database: PDB / ID: 6bua
TitleDrosophila Dicer-2 apo homology model (helicase, Platform-PAZ, RNaseIII domains)
ComponentsDicer-2, isoform A
KeywordsRNA BINDING PROTEIN / Dicer / dmDcr2 / Dicer-2 / helicase / platform / PAZ / RNAseIII
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 / adenosinetriphosphatase / siRNA loading onto RISC involved in RNA interference / detection of virus / RISC-loading complex / ribonuclease III activity / production of siRNA involved in RNA interference / 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 sourceDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.1 Å resolution
AuthorsShen, P.S. / Sinha, N.K. / Bass, B.L.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Dec 9, 2017 / Release: Dec 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 27, 2017Structure modelrepositoryInitial release
1.1Jan 3, 2018Structure modelDatabase referencescitation_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
1.2Jan 17, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization
1.3Jan 31, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Assembly

Deposited unit
A: Dicer-2, isoform A


Theoretical massNumber of molelcules
Total (without water)198,0751
Polyers198,0751
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

#1: Protein/peptide Dicer-2, isoform A / / FI15132p1


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Drosophila Dicer-2 (apo) / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 85119 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0014659
ELECTRON MICROSCOPYf_angle_d0.3396481
ELECTRON MICROSCOPYf_dihedral_angle_d1.7382735
ELECTRON MICROSCOPYf_chiral_restr0.040902
ELECTRON MICROSCOPYf_plane_restr0.001931

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