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Yorodumi- PDB-7vg2: Cryo-EM structure of Arabidopsis DCL3 in complex with a 40-bp RNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vg2 | ||||||
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Title | Cryo-EM structure of Arabidopsis DCL3 in complex with a 40-bp RNA | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / DCL3 / RNA / RdDM / Dicer / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information ribonuclease III activity / regulatory ncRNA-mediated gene silencing / RNA processing / RNA binding / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Wang, Q. / Du, J. | ||||||
Citation | Journal: Science / Year: 2021 Title: Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation. Authors: Qian Wang / Yan Xue / Laixing Zhang / Zhenhui Zhong / Suhua Feng / Changshi Wang / Lifan Xiao / Zhenlin Yang / C Jake Harris / Zhe Wu / Jixian Zhai / Maojun Yang / Sisi Li / Steven E Jacobsen / Jiamu Du / Abstract: In eukaryotes, small RNAs (sRNAs) play critical roles in multiple biological processes. Dicer endonucleases are a central part of sRNA biogenesis. In plants, DICER-LIKE PROTEIN 3 (DCL3) produces 24- ...In eukaryotes, small RNAs (sRNAs) play critical roles in multiple biological processes. Dicer endonucleases are a central part of sRNA biogenesis. In plants, DICER-LIKE PROTEIN 3 (DCL3) produces 24-nucleotide (nt) small interfering RNAs (siRNAs) that determine the specificity of the RNA-directed DNA methylation pathway. Here, we determined the structure of a DCL3–pre-siRNA complex in an active dicing-competent state. The 5′-phosphorylated A1 of the guide strand and the 1-nt 3′ overhang of the complementary strand are specifically recognized by a positively charged pocket and an aromatic cap, respectively. The 24-nt siRNA length dependence relies on the separation between the 5′-phosphorylated end of the guide RNA and dual cleavage sites formed by the paired ribonuclease III domains. These structural studies, complemented by functional data, provide insight into the dicing principle for Dicers in general. | ||||||
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 | 7vg2.cif.gz | 216.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vg2.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 7vg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vg2_validation.pdf.gz | 754.9 KB | Display | wwPDB validaton report |
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Full document | 7vg2_full_validation.pdf.gz | 778.5 KB | Display | |
Data in XML | 7vg2_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 7vg2_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/7vg2 ftp://data.pdbj.org/pub/pdb/validation_reports/vg/7vg2 | HTTPS FTP |
-Related structure data
Related structure data | 31963MC 7vg3C 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: 182176.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DCL3, ATDCL3, DICER-LIKE 3, dicer-like 3, At3g43920 / Plasmid: pFastHTB / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F4J0I5 | ||||
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#2: RNA chain | Mass: 12812.680 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) | ||||
#3: RNA chain | Mass: 13042.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) | ||||
#4: Chemical | #5: Chemical | ChemComp-ZN / | Has ligand of interest | Y | |
-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 |
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Molecular weight | Value: 0.21 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Arabidopsis thaliana (thale cress) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.8 mg/ml / 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: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 220948 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL |