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Yorodumi- PDB-7eld: Cryo-EM structure of Arabidopsis DCL1 in complex with pri-miRNA 166f -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eld | ||||||
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Title | Cryo-EM structure of Arabidopsis DCL1 in complex with pri-miRNA 166f | ||||||
Components |
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Keywords | HYDROLASE / MicroRNA / miRNA / Endonuclease / Helicase / Nuclease / RNA-binding | ||||||
Function / homology | Function and homology information ta-siRNA processing / ribonuclease III activity / siRNA processing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / helicase activity / rRNA processing / double-stranded RNA binding / DNA binding / RNA binding / ATP binding ...ta-siRNA processing / ribonuclease III activity / siRNA processing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / helicase activity / rRNA processing / double-stranded RNA binding / DNA binding / RNA binding / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
Authors | Wei, X. / Ke, H. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Plants / Year: 2021 Title: Structural basis of microRNA processing by Dicer-like 1. Authors: Xiaobin Wei / Huanhuan Ke / Aijia Wen / Bo Gao / Jing Shi / Yu Feng / Abstract: MicroRNAs (miRNAs) are short non-coding RNAs that inhibit the expression of target genes by directly binding to their mRNAs. In animals, pri-miRNAs are cleaved by Drosha to generate pre-miRNAs, which ...MicroRNAs (miRNAs) are short non-coding RNAs that inhibit the expression of target genes by directly binding to their mRNAs. In animals, pri-miRNAs are cleaved by Drosha to generate pre-miRNAs, which are subsequently cleaved by Dicer to generate mature miRNAs. Instead of being cleaved by two different enzymes, both cleavages in plants are performed by Dicer-like 1 (DCL1). With a similar domain architecture as human Dicer, it is mysterious how DCL1 recognizes pri-miRNAs and performs two cleavages sequentially. Here, we report the single-particle cryo-electron microscopy structures of Arabidopsis DCL1 complexed with a pri-miRNA and a pre-miRNA, respectively, in cleavage-competent states. These structures uncover the plasticity of the PAZ domain, which is critical for the recognition of both pri-miRNA and pre-miRNA. These structures suggest that the helicase module serves as an engine that transfers the substrate between two sequential cleavage events. This study lays a foundation for dissecting the regulation mechanism of miRNA biogenesis in plants and provides insights into the dicing state of human Dicer. | ||||||
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 | 7eld.cif.gz | 281.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eld.ent.gz | 207.8 KB | Display | PDB format |
PDBx/mmJSON format | 7eld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eld_validation.pdf.gz | 771.1 KB | Display | wwPDB validaton report |
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Full document | 7eld_full_validation.pdf.gz | 794 KB | Display | |
Data in XML | 7eld_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 7eld_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/7eld ftp://data.pdbj.org/pub/pdb/validation_reports/el/7eld | HTTPS FTP |
-Related structure data
Related structure data | 31181MC 7eleC 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: 213859.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DCL1, ASU1, CAF SIN1, SUS1, At1g01040, T25K16.4 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9SP32, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters |
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#2: RNA chain | Mass: 47200.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: GenBank: 3449316 |
-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: Binary complex of DCL1 in complex with pri-miRNA 166f / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 653929 / Symmetry type: POINT |