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Yorodumi- PDB-8dfv: Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partne... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dfv | ||||||||||||
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Title | Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB - complex IIa | ||||||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / Dicer / Dcr-1 / Loquacious / Loqs-P / miRNA / RNA BINDING PROTEIN-RNA complex | ||||||||||||
Function / homology | Function and homology information mitotic cell cycle, embryonic / germarium-derived female germ-line cyst formation / germarium-derived oocyte fate determination / germ-line stem cell division / bidentate ribonuclease III activity / MicroRNA (miRNA) biogenesis / pole cell formation / regulatory ncRNA processing / Small interfering RNA (siRNA) biogenesis / female germ-line stem cell asymmetric division ...mitotic cell cycle, embryonic / germarium-derived female germ-line cyst formation / germarium-derived oocyte fate determination / germ-line stem cell division / bidentate ribonuclease III activity / MicroRNA (miRNA) biogenesis / pole cell formation / regulatory ncRNA processing / Small interfering RNA (siRNA) biogenesis / female germ-line stem cell asymmetric division / segment polarity determination / PKR-mediated signaling / dsRNA transport / regulation of regulatory ncRNA processing / RISC complex binding / dosage compensation by hyperactivation of X chromosome / pre-miRNA binding / germ-line stem cell population maintenance / ribonuclease III / deoxyribonuclease I activity / apoptotic DNA fragmentation / miRNA metabolic process / RISC-loading complex / regulatory ncRNA-mediated post-transcriptional gene silencing / RISC complex assembly / miRNA processing / pre-miRNA processing / ribonuclease III activity / siRNA processing / siRNA binding / RISC complex / dendrite morphogenesis / response to starvation / helicase activity / central nervous system development / double-stranded RNA binding / single-stranded RNA binding / RNA binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å | ||||||||||||
Authors | Jouravleva, K. / Golovenko, D. / Demo, G. / Dutcher, R.C. / Tanaka Hall, T.M. / Zamore, P.D. / Korostelev, A.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB. Authors: Karina Jouravleva / Dmitrij Golovenko / Gabriel Demo / Robert C Dutcher / Traci M Tanaka Hall / Phillip D Zamore / Andrei A Korostelev / Abstract: In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM ...In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 that show how Dicer-1 and its partner Loqs‑PB cooperate (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, and (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicer‑1⋅Loqs‑PB heterodimer. The Dicer-1 dsRBD and three Loqs‑PB dsRBDs form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-miRNA cleavage shifts the dsRBDs and partially closes Dicer-1, which may promote product release. Our data suggest a model for how the Dicer‑1⋅Loqs‑PB complex affects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and product release. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dfv.cif.gz | 534.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dfv.ent.gz | 341.8 KB | Display | PDB format |
PDBx/mmJSON format | 8dfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/8dfv ftp://data.pdbj.org/pub/pdb/validation_reports/df/8dfv | HTTPS FTP |
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-Related structure data
Related structure data | 27415MC 8dg5C 8dg7C 8dgaC 8dgiC 8dgjC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 255733.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dcr-1, CG4792 / Production host: unidentified baculovirus References: UniProt: Q9VCU9, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters | ||
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#2: RNA chain | Mass: 19102.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) | ||
#3: Protein | Mass: 50149.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG6866 / Production host: unidentified baculovirus / References: UniProt: Q9VJY9 | ||
#4: Chemical | ChemComp-CA / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary complex of Dicer-1 and Loqs-PB binding pre-miRNA Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Source (recombinant) | Organism: unidentified baculovirus |
Buffer solution | pH: 7.9 |
Buffer component | Conc.: 20 mM / Name: HEPES-KOH / Formula: HEPES-KOH |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 65.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2023692 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149443 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.84 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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