+Open data
-Basic information
Entry | Database: PDB / ID: 6lxe | |||||||||||||||||||||
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Title | DROSHA-DGCR8 complex | |||||||||||||||||||||
Components |
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Keywords | HYDROLASE/RNA BINDING PROTEIN / Ribonuclease / RNA BINDING PROTEIN / HYDROLASE-RNA BINDING PROTEIN complex | |||||||||||||||||||||
Function / homology | Function and homology information positive regulation of pre-miRNA processing / regulation of miRNA metabolic process / protein-RNA adaptor activity / DEAD/H-box RNA helicase binding / primary miRNA binding / regulation of regulatory T cell differentiation / Transcriptional Regulation by MECP2 / ribonuclease III / miRNA metabolic process / primary miRNA processing ...positive regulation of pre-miRNA processing / regulation of miRNA metabolic process / protein-RNA adaptor activity / DEAD/H-box RNA helicase binding / primary miRNA binding / regulation of regulatory T cell differentiation / Transcriptional Regulation by MECP2 / ribonuclease III / miRNA metabolic process / primary miRNA processing / regulation of stem cell proliferation / ribonuclease III activity / microprocessor complex / pre-miRNA processing / R-SMAD binding / MicroRNA (miRNA) biogenesis / SMAD binding / lipopolysaccharide binding / rRNA processing / double-stranded RNA binding / regulation of inflammatory response / protein-macromolecule adaptor activity / site of double-strand break / defense response to Gram-negative bacterium / postsynaptic density / nuclear body / defense response to Gram-positive bacterium / DNA damage response / glutamatergic synapse / heme binding / positive regulation of gene expression / nucleolus / protein homodimerization activity / RNA binding / nucleoplasm / 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: 4.2 Å | |||||||||||||||||||||
Authors | Jin, W. / Wang, J. / Liu, C.P. / Wang, H.W. / Xu, R.M. | |||||||||||||||||||||
Funding support | China, 6items
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Citation | Journal: Mol Cell / Year: 2020 Title: Structural Basis for pri-miRNA Recognition by Drosha. Authors: Wenxing Jin / Jia Wang / Chao-Pei Liu / Hong-Wei Wang / Rui-Ming Xu / Abstract: A commencing and critical step in miRNA biogenesis involves processing of pri-miRNAs in the nucleus by Microprocessor. An important, but not completely understood, question is how Drosha, the ...A commencing and critical step in miRNA biogenesis involves processing of pri-miRNAs in the nucleus by Microprocessor. An important, but not completely understood, question is how Drosha, the catalytic subunit of Microprocessor, binds pri-miRNAs and correctly specifies cleavage sites. Here we report the cryoelectron microscopy structures of the Drosha-DGCR8 complex with and without a pri-miRNA. The RNA-bound structure provides direct visualization of the tertiary structure of pri-miRNA and shows that a helix hairpin in the extended PAZ domain and the mobile basic (MB) helix in the RNase IIIa domain of Drosha coordinate to recognize the single-stranded to double-stranded junction of RNA, whereas the dsRNA binding domain makes extensive contacts with the RNA stem. Furthermore, the RNA-free structure reveals an autoinhibitory conformation of the PAZ helix hairpin. These findings provide mechanistic insights into pri-miRNA cleavage site selection and conformational dynamics governing pri-miRNA recognition by the catalytic component of Microprocessor. | |||||||||||||||||||||
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 | 6lxe.cif.gz | 233.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lxe.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 6lxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lxe_validation.pdf.gz | 709.2 KB | Display | wwPDB validaton report |
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Full document | 6lxe_full_validation.pdf.gz | 726.3 KB | Display | |
Data in XML | 6lxe_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 6lxe_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/6lxe ftp://data.pdbj.org/pub/pdb/validation_reports/lx/6lxe | HTTPS FTP |
-Related structure data
Related structure data | 30006MC 6lxdC 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: 115390.578 Da / Num. of mol.: 1 / Mutation: E1045Q, E1222Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DROSHA, RN3, RNASE3L, RNASEN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NRR4, ribonuclease III | ||||
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#2: Protein | Mass: 86171.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DGCR8, C22orf12, DGCRK6, LP4941 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WYQ5 #3: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary complex of DROSHA-DGCR8 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.3 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 % |
-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 / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / 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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109333 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 5B16 Accession code: 5B16 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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