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Yorodumi- PDB-6bua: Drosophila Dicer-2 apo homology model (helicase, Platform-PAZ, RN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bua | ||||||
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Title | Drosophila Dicer-2 apo homology model (helicase, Platform-PAZ, RNaseIII domains) | ||||||
Components | Dicer-2, isoform A | ||||||
Keywords | RNA BINDING PROTEIN / Dicer / dmDcr2 / Dicer-2 / helicase / platform / PAZ / RNAseIII | ||||||
Function / homology | Function and homology information bidentate ribonuclease III activity / positive regulation of Toll signaling pathway / dsRNA transport / dosage compensation by hyperactivation of X chromosome / global gene silencing by mRNA cleavage / ribonuclease III / deoxyribonuclease I activity / apoptotic DNA fragmentation / detection of virus / RISC-loading complex ...bidentate ribonuclease III activity / positive regulation of Toll signaling pathway / dsRNA transport / dosage compensation by hyperactivation of X chromosome / global gene silencing by mRNA cleavage / ribonuclease III / deoxyribonuclease I activity / apoptotic DNA fragmentation / detection of virus / RISC-loading complex / regulatory ncRNA-mediated post-transcriptional gene silencing / RISC complex assembly / ribonuclease III activity / siRNA processing / siRNA binding / ATP-dependent activity, acting on RNA / positive regulation of innate immune response / RISC complex / heterochromatin formation / positive regulation of defense response to virus by host / locomotory behavior / helicase activity / mRNA 3'-UTR binding / cellular response to virus / cytoplasmic ribonucleoprotein granule / defense response to virus / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å | ||||||
Authors | Shen, P.S. / Sinha, N.K. / Bass, B.L. | ||||||
Funding support | United States, 1items
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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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6bua.cif.gz | 159.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bua.ent.gz | 92.4 KB | Display | PDB format |
PDBx/mmJSON format | 6bua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/6bua ftp://data.pdbj.org/pub/pdb/validation_reports/bu/6bua | HTTPS FTP |
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-Related structure data
Related structure data | 7291MC 7290C 7292C 6bu9C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 198074.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source 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, EC: 3.6.1.3 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Drosophila Dicer-2 (apo) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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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
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
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) |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85119 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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