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- PDB-8dg5: Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partne... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dg5 | ||||||||||||
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Title | Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB - complex IIb | ||||||||||||
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![]() | RNA BINDING PROTEIN/RNA / Dicer / Dcr-1 / Loquacious / Loqs-PB / miRNA / RNA BINDING PROTEIN-RNA complex | ||||||||||||
Function / homology | ![]() 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 / regulatory ncRNA processing / MicroRNA (miRNA) biogenesis / pole cell formation / 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 / regulatory ncRNA processing / MicroRNA (miRNA) biogenesis / pole cell formation / Small interfering RNA (siRNA) biogenesis / female germ-line stem cell asymmetric division / segment polarity determination / PKR-mediated signaling / regulation of regulatory ncRNA processing / dsRNA transport / dosage compensation by hyperactivation of X chromosome / RISC complex binding / pre-miRNA binding / germ-line stem cell population maintenance / ribonuclease III / apoptotic DNA fragmentation / miRNA metabolic process / RISC-loading complex / deoxyribonuclease I activity / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / ribonuclease III activity / miRNA processing / siRNA binding / pre-miRNA processing / siRNA processing / RISC complex / dendrite morphogenesis / response to starvation / RNA endonuclease activity / helicase activity / central nervous system development / double-stranded RNA binding / single-stranded RNA binding / RNA binding / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å | ||||||||||||
![]() | Jouravleva, K. / Golovenko, D. / Demo, G. / Dutcher, R.C. / Tanaka Hall, T.M. / Zamore, P.D. / Korostelev, A.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 529.9 KB | Display | ![]() |
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PDB format | ![]() | 333.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 66.2 KB | Display | |
Data in CIF | ![]() | 98.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27416MC ![]() 8dfvC ![]() 8dg7C ![]() 8dgaC ![]() 8dgiC ![]() 8dgjC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: Q9VCU9, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters | ||||
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#2: RNA chain | Mass: 18796.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||
#3: Protein | Mass: 50149.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-U5P / | 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 |
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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: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
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: 293 K |
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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 / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 66.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3161540 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185002 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.54 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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