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Yorodumi- PDB-7zpk: Mammalian Dicer in the "pre-dicing state" with pre-miR-15a substr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zpk | |||||||||
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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 / 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 RNA metabolic process / regulation of regulatory ncRNA processing / peripheral nervous system myelin formation / negative regulation of defense response to virus by host / regulation of epithelial cell differentiation / pre-miRNA binding / regulation of regulatory T cell differentiation / regulation of Notch signaling pathway / spinal cord motor neuron differentiation / global gene silencing by mRNA cleavage / 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 / nerve development / meiotic spindle organization / positive regulation of Schwann cell differentiation / RISC-loading complex / deoxyribonuclease I activity / RISC complex assembly / intestinal epithelial cell development / ribonuclease III activity / regulatory ncRNA-mediated post-transcriptional gene silencing / pericentric heterochromatin formation / miRNA processing / regulation of stem cell differentiation / siRNA binding / pre-miRNA processing / regulation of viral genome replication / siRNA processing / neural precursor cell proliferation / digestive tract development / mRNA stabilization / embryonic hindlimb morphogenesis / cartilage development / cardiac muscle cell development / RISC complex / embryonic limb morphogenesis / miRNA binding / positive regulation of vascular endothelial cell proliferation / regulation of myelination / regulation of neuron differentiation / negative regulation of glial cell proliferation / hair follicle morphogenesis / stem cell population maintenance / branching morphogenesis of an epithelial tube / positive regulation of miRNA metabolic process / positive regulation of muscle cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / spermatid development / regulation of neurogenesis / hair follicle development / single fertilization / positive regulation of collagen biosynthetic process / postsynaptic density, intracellular component / spindle assembly / positive regulation of viral genome replication / RNA processing / spleen development / positive regulation of endothelial cell migration / helicase activity / neuron projection morphogenesis / post-embryonic development / positive regulation of translation / regulation of protein phosphorylation / lung development / multicellular organism growth / cerebral cortex development / rRNA processing / double-stranded RNA binding / gene expression / growth cone / regulation of inflammatory response / 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 | 7zpk.cif.gz | 572.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zpk.ent.gz | 453.8 KB | Display | PDB format |
PDBx/mmJSON format | 7zpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zpk_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7zpk_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7zpk_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 7zpk_validation.cif.gz | 77.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/7zpk ftp://data.pdbj.org/pub/pdb/validation_reports/zp/7zpk | HTTPS FTP |
-Related structure data
Related structure data | 14856MC 7yymC 7yynC 7yz4C 7zpiC 7zpjC 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: Correlation coefficient Details: Initial model used from PDB ID:7ZPJ TARBP2 dsRBD domain 1: initial model from PDB ID:7ZPJ TARBP2 dsRBD domains 2,3: manually fitted into EM map according to map density | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Accession code: 7ZPJ / Initial refinement model-ID: 1 / PDB-ID: 7ZPJ / Source name: PDB / Type: experimental model
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Refine LS restraints |
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