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Open data
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Basic information
Entry | Database: PDB / ID: 6bu9 | ||||||
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Title | Drosophila Dicer-2 bound to blunt dsRNA | ||||||
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![]() | rna binding protein/rna / Dicer / Dcr2 / Dcr-2 / dmDcr-2 / Dicer-2 / helicase / dsRNA / RNA / RNA BINDING PROTEIN / rna binding protein-rna complex | ||||||
Function / homology | ![]() lncRNA catabolic process / 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 / apoptotic DNA fragmentation / RISC-loading complex / detection of virus ...lncRNA catabolic process / 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 / apoptotic DNA fragmentation / RISC-loading complex / detection of virus / deoxyribonuclease I activity / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / ribonuclease III activity / siRNA binding / siRNA processing / 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 / helicase activity / mRNA 3'-UTR binding / locomotory behavior / 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 | ![]() ![]() unidentified (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.8 Å | ||||||
![]() | Shen, P.S. / Sinha, N.K. / Bass, B.L. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.3 KB | Display | ![]() |
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PDB format | ![]() | 64 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.7 KB | Display | ![]() |
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Full document | ![]() | 759.3 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7290MC ![]() 7291C ![]() 7292C ![]() 6buaC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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#2: RNA chain | Mass: 16781.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) |
#3: RNA chain | Mass: 16528.768 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Drosophila Dicer-2 bound to blunt dsRNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: FEI TECNAI 20 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19445 / Symmetry type: POINT |