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- PDB-7v6c: Structure of the Dicer-2-R2D2 heterodimer bound to small RNA duplex -
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Open data
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Basic information
Entry | Database: PDB / ID: 7v6c | ||||||
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Title | Structure of the Dicer-2-R2D2 heterodimer bound to small RNA duplex | ||||||
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![]() | RNA BINDING PROTEIN / Ribonuclease / Double-stranded RNA-binding protein | ||||||
Function / homology | ![]() follicle cell of egg chamber stalk formation / lncRNA catabolic process / : / positive regulation of Toll signaling pathway / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / PKR-mediated signaling / regulation of regulatory ncRNA processing / dsRNA transport / dosage compensation by hyperactivation of X chromosome ...follicle cell of egg chamber stalk formation / lncRNA catabolic process / : / positive regulation of Toll signaling pathway / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / PKR-mediated signaling / regulation of regulatory ncRNA processing / dsRNA transport / dosage compensation by hyperactivation of X chromosome / global gene silencing by mRNA cleavage / ribonuclease III / apoptotic DNA fragmentation / deoxyribonuclease I activity / RISC-loading complex / detection of virus / 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 / positive regulation of defense response to virus by host / helicase activity / locomotory behavior / mRNA 3'-UTR binding / heterochromatin formation / cellular response to virus / cytoplasmic ribonucleoprotein granule / double-stranded RNA binding / defense response to virus / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
![]() | Yamaguchi, S. / Nishizawa, T. / Kusakizako, T. / Yamashita, K. / Tomita, A. / Hirano, H. / Nishimasu, H. / Nureki, O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the Dicer-2-R2D2 heterodimer bound to a small RNA duplex. Authors: Sonomi Yamaguchi / Masahiro Naganuma / Tomohiro Nishizawa / Tsukasa Kusakizako / Yukihide Tomari / Hiroshi Nishimasu / Osamu Nureki / ![]() Abstract: In flies, Argonaute2 (Ago2) and small interfering RNA (siRNA) form an RNA-induced silencing complex to repress viral transcripts. The RNase III enzyme Dicer-2 associates with its partner protein R2D2 ...In flies, Argonaute2 (Ago2) and small interfering RNA (siRNA) form an RNA-induced silencing complex to repress viral transcripts. The RNase III enzyme Dicer-2 associates with its partner protein R2D2 and cleaves long double-stranded RNAs to produce 21-nucleotide siRNA duplexes, which are then loaded into Ago2 in a defined orientation. Here we report cryo-electron microscopy structures of the Dicer-2-R2D2 and Dicer-2-R2D2-siRNA complexes. R2D2 interacts with the helicase domain and the central linker of Dicer-2 to inhibit the promiscuous processing of microRNA precursors by Dicer-2. Notably, our structure represents the strand-selection state in the siRNA-loading process, and reveals that R2D2 asymmetrically recognizes the end of the siRNA duplex with the higher base-pairing stability, and the other end is exposed to the solvent and is accessible by Ago2. Our findings explain how R2D2 senses the thermodynamic asymmetry of the siRNA and facilitates the siRNA loading into Ago2 in a defined orientation, thereby determining which strand of the siRNA duplex is used by Ago2 as the guide strand for target silencing. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 418 KB | Display | ![]() |
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PDB format | ![]() | 321.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 31742MC ![]() 7v6bC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() Data size: 1.4 TB Data #1: Structure of the Dicer-2-R2D2 heterodimer [micrographs - multiframe] Data #2: Structure of the Dicer-2-R2D2 heterodimer bound to small RNA duplex [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 199309.000 Da / Num. of mol.: 1 / Mutation: M208L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Dcr-2, cg6493, Dcr, dcr, DCR-2, dcr-2, Dcr-2-RA, DCR2, Dcr2, dcr2, dDcr2, dic2, DICER, Dicer, dicer, DICER-2, dicer-2, Dicer2, dicer2, dmDcr-2, Dmel\CG6493, CG6493, Dmel_CG6493 Production host: ![]() ![]() References: UniProt: A1ZAW0, deoxyribonuclease I, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters, ribonuclease III, EC: 3.6.1.3 |
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#2: Protein | Mass: 39920.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: r2d2, cg7138, Dmel\CG7138, R2D2, R2d2, CG7138, Dmel_CG7138 Production host: ![]() ![]() |
-RNA chain , 4 types, 4 molecules EFCD
#3: RNA chain | Mass: 6812.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#4: RNA chain | Mass: 6514.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#5: RNA chain | Mass: 7141.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#6: RNA chain | Mass: 6820.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-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: Dicer-2-R2D2-siRNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: REFMAC / Version: 5.8.0267 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144979 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.3→165.75 Å / Cor.coef. Fo:Fc: 0.943 / SU B: 16.404 / SU ML: 0.268 / ESU R: 0.423 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 101.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 15643 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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