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Yorodumi- PDB-7zpj: Mammalian Dicer in the "pre-dicing state" with pre-miR-15a substr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zpj | |||||||||
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Title | Mammalian Dicer in the "pre-dicing state" with pre-miR-15a substrate and TARBP2 subunit | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN / endoribonuclease / dsRNA / complex / gene silencing / post-transcriptional / catalytic complex / cytoplasm / RISC-loading complex / TARBP2 RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information regulation of muscle cell apoptotic process / myoblast differentiation involved in skeletal muscle regeneration / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / regulation of siRNA processing / regulation of miRNA processing / ganglion development / hair follicle cell proliferation / zygote asymmetric cell division / regulation of oligodendrocyte differentiation ...regulation of muscle cell apoptotic process / myoblast differentiation involved in skeletal muscle regeneration / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / regulation of siRNA processing / regulation of miRNA processing / ganglion development / hair follicle cell proliferation / zygote asymmetric cell division / regulation of oligodendrocyte differentiation / cardiac neural crest cell development involved in outflow tract morphogenesis / positive regulation of endothelial cell-matrix adhesion via fibronectin / olfactory bulb interneuron differentiation / regulation of enamel mineralization / regulation of viral transcription / positive regulation of establishment of endothelial barrier / regulation of RNA metabolic process / positive regulation of hepatic stellate cell proliferation / trophectodermal cell proliferation / regulation of miRNA metabolic process / regulation of odontogenesis of dentin-containing tooth / spermatogonial cell division / regulation of regulatory ncRNA processing / peripheral nervous system myelin formation / negative regulation of defense response to virus by host / PKR-mediated signaling / regulation of epithelial cell differentiation / pre-miRNA binding / regulation of regulatory T cell differentiation / global gene silencing by mRNA cleavage / spinal cord motor neuron differentiation / regulation of Notch signaling pathway / epidermis morphogenesis / negative regulation of Schwann cell proliferation / reproductive structure development / ribonuclease III / positive regulation of myelination / apoptotic DNA fragmentation / inner ear receptor cell development / skeletal muscle tissue regeneration / deoxyribonuclease I activity / nerve development / meiotic spindle organization / positive regulation of Schwann cell differentiation / RISC-loading complex / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / ribonuclease III activity / intestinal epithelial cell development / miRNA processing / pre-miRNA processing / pericentric heterochromatin formation / regulation of stem cell differentiation / siRNA binding / siRNA processing / regulation of viral genome replication / neural precursor cell proliferation / digestive tract development / RISC complex / mRNA stabilization / embryonic hindlimb morphogenesis / cartilage development / cardiac muscle cell development / embryonic limb morphogenesis / miRNA binding / positive regulation of miRNA metabolic process / positive regulation of vascular endothelial cell proliferation / regulation of neuron differentiation / regulation of myelination / negative regulation of glial cell proliferation / hair follicle morphogenesis / stem cell population maintenance / branching morphogenesis of an epithelial tube / positive regulation of muscle cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / spermatid development / regulation of neurogenesis / hair follicle development / positive regulation of collagen biosynthetic process / single fertilization / spindle assembly / postsynaptic density, intracellular component / positive regulation of viral genome replication / RNA processing / spleen development / positive regulation of endothelial cell migration / neuron projection morphogenesis / post-embryonic development / helicase activity / positive regulation of translation / regulation of protein phosphorylation / lung development / multicellular organism growth / cerebral cortex development / rRNA processing / double-stranded RNA binding / gene expression / regulation of inflammatory response / growth cone / regulation of gene expression Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å | |||||||||
Authors | Zanova, M. / Zapletal, D. / Kubicek, K. / Stefl, R. / Pinkas, M. / Novacek, J. | |||||||||
Funding support | Czech Republic, 2items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structural and functional basis of mammalian microRNA biogenesis by Dicer. Authors: David Zapletal / Eliska Taborska / Josef Pasulka / Radek Malik / Karel Kubicek / Martina Zanova / Christian Much / Marek Sebesta / Valeria Buccheri / Filip Horvat / Irena Jenickova / ...Authors: David Zapletal / Eliska Taborska / Josef Pasulka / Radek Malik / Karel Kubicek / Martina Zanova / Christian Much / Marek Sebesta / Valeria Buccheri / Filip Horvat / Irena Jenickova / Michaela Prochazkova / Jan Prochazka / Matyas Pinkas / Jiri Novacek / Diego F Joseph / Radislav Sedlacek / Carrie Bernecky / Dónal O'Carroll / Richard Stefl / Petr Svoboda / Abstract: MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is ...MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer's DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer•-miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zpj.cif.gz | 525.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zpj.ent.gz | 411.5 KB | Display | PDB format |
PDBx/mmJSON format | 7zpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/7zpj ftp://data.pdbj.org/pub/pdb/validation_reports/zp/7zpj | HTTPS FTP |
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-Related structure data
Related structure data | 14855MC 7yymC 7yynC 7yz4C 7zpiC 7zpkC C: citing same article (ref.) M: map data used to model this data |
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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: 226925.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dicer1, Dicer, Mdcr / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8R418, ribonuclease III |
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#2: RNA chain | Mass: 19017.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: from Mus musculus / Source: (synth.) Mus musculus (house mouse) / References: GenBank: 262205589 |
#3: Protein | Mass: 39991.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tarbp2, Prbp / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P97473 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 Details: The buffer was always prepared fresh in RNAse-free manner. | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Described in STAR methods |
-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 FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 60.198 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 48253 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2219694 | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 437518 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 189.2 / Protocol: FLEXIBLE FIT / Space: REAL Target criteria: Ramachandran Plot, Rotamer Analysis, Density Fit Analysis, Correlation coefficient Details: We used our previous deposition 7YYM as an initial model source. TARBP2 initial coordinates were predicted by AlphaFold. Initial local fitting was done using Chimera and then Coot's Real ...Details: We used our previous deposition 7YYM as an initial model source. TARBP2 initial coordinates were predicted by AlphaFold. Initial local fitting was done using Chimera and then Coot's Real Space Refine Zone. PHENIX Real-space refinement was used for flexible fitting. ISOLDE was used for flexible fitting with torsion restraints defined for polypeptide chain and distance restraints for polyribonucleotides. | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Accession code: 7YYM / Initial refinement model-ID: 1 / PDB-ID: 7YYM / Source name: PDB / Type: experimental model
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Refine LS restraints |
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