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Yorodumi- PDB-5zak: Cryo-EM structure of human Dicer and its complexes with a pre-miR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zak | ||||||
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Title | Cryo-EM structure of human Dicer and its complexes with a pre-miRNA substrate | ||||||
Components |
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Keywords | HYDROLASE/PROTEIN BINDING / Dicer / TRBP / Cryo-EM / RNA interference / HYDROLASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information regulation of siRNA processing / regulation of miRNA processing / regulation of viral transcription / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of regulatory ncRNA processing / peripheral nervous system myelin formation / negative regulation of defense response to virus by host / pre-miRNA binding / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / global gene silencing by mRNA cleavage ...regulation of siRNA processing / regulation of miRNA processing / regulation of viral transcription / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of regulatory ncRNA processing / peripheral nervous system myelin formation / negative regulation of defense response to virus by host / pre-miRNA binding / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / global gene silencing by mRNA cleavage / Small interfering RNA (siRNA) biogenesis / tRNA decay / negative regulation of Schwann cell proliferation / ribonuclease III / positive regulation of myelination / apoptotic DNA fragmentation / deoxyribonuclease I activity / nerve development / positive regulation of Schwann cell differentiation / RISC-loading complex / miRNA metabolic process / RISC complex assembly / ribonuclease III activity / miRNA processing / pre-miRNA processing / siRNA binding / siRNA processing / Regulation of MITF-M-dependent genes involved in apoptosis / M-decay: degradation of maternal mRNAs by maternally stored factors / pre-mRNA binding / RISC complex / MicroRNA (miRNA) biogenesis / miRNA binding / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of viral genome replication / neuron projection morphogenesis / protein sequestering activity / RNA endonuclease activity / helicase activity / negative regulation of protein kinase activity / PKR-mediated signaling / double-stranded RNA binding / regulation of translation / nuclear body / protein domain specific binding / negative regulation of gene expression / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
Authors | Liu, Z. / Wang, J. / Cheng, H. / Ke, X. / Sun, L. / Zhang, Q.C. / Wang, H.-W. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell / Year: 2018 Title: Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate. Authors: Zhongmin Liu / Jia Wang / Hang Cheng / Xin Ke / Lei Sun / Qiangfeng Cliff Zhang / Hong-Wei Wang / Abstract: Human Dicer (hDicer) is a multi-domain protein belonging to the RNase III family. It plays pivotal roles in small RNA biogenesis during the RNA interference (RNAi) pathway by processing a diverse ...Human Dicer (hDicer) is a multi-domain protein belonging to the RNase III family. It plays pivotal roles in small RNA biogenesis during the RNA interference (RNAi) pathway by processing a diverse range of double-stranded RNA (dsRNA) precursors to generate ∼22 nt microRNA (miRNA) or small interfering RNA (siRNA) products for sequence-directed gene silencing. In this work, we solved the cryoelectron microscopy (cryo-EM) structure of hDicer in complex with its cofactor protein TRBP and revealed the precise spatial arrangement of hDicer's multiple domains. We further solved structures of the hDicer-TRBP complex bound with pre-let-7 RNA in two distinct conformations. In combination with biochemical analysis, these structures reveal a property of the hDicer-TRBP complex to promote the stability of pre-miRNA's stem duplex in a pre-dicing state. These results provide insights into the mechanism of RNA processing by hDicer and illustrate the regulatory role of hDicer's N-terminal helicase domain. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5zak.cif.gz | 273.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zak.ent.gz | 213.4 KB | Display | PDB format |
PDBx/mmJSON format | 5zak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zak_validation.pdf.gz | 720.4 KB | Display | wwPDB validaton report |
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Full document | 5zak_full_validation.pdf.gz | 755.9 KB | Display | |
Data in XML | 5zak_validation.xml.gz | 45.7 KB | Display | |
Data in CIF | 5zak_validation.cif.gz | 68.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/5zak ftp://data.pdbj.org/pub/pdb/validation_reports/za/5zak | HTTPS FTP |
-Related structure data
Related structure data | 6904MC 6905C 6906C 5zalC 5zamC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 218947.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TARBP2, TRBP / Production host: Homo sapiens (human) / References: UniProt: Q9UPY3, ribonuclease III |
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#2: Protein | Mass: 39085.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q15633 |
-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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Buffer solution | pH: 8 Details: 50 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM DTT, 2 mM EDTA | ||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono-disperse. | ||||||||||||||||||
Specimen support | Details: The grid was glow-discharged prior to use. / Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 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 FIELD / Nominal magnification: 22500 X / Calibrated magnification: 38462 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2500 nm / Calibrated defocus min: 2500 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 80 K |
Image recording | Average exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7581 |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 32 / Used frames/image: 1-32 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 337566 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 100 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: CC | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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