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Yorodumi- PDB-8hil: A cryo-EM structure of B. oleracea RNA polymerase V at 3.57 Angstrom -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hil | ||||||
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Title | A cryo-EM structure of B. oleracea RNA polymerase V at 3.57 Angstrom | ||||||
Components |
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Keywords | TRANSCRIPTION / DNA-dependent RNA polymerase V | ||||||
Function / homology | Function and homology information : / RNA polymerase V complex / RNA polymerase II activity / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / nucleic acid binding / protein dimerization activity ...: / RNA polymerase V complex / RNA polymerase II activity / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / nucleic acid binding / protein dimerization activity / DNA-templated transcription / nucleolus / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Brassica oleracea (wild cabbage) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å | ||||||
Authors | Du, X. / Xie, G. / Hu, H. / Du, J. | ||||||
Funding support | 1items
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Citation | Journal: Science / Year: 2023 Title: Structure and mechanism of the plant RNA polymerase V. Authors: Guohui Xie / Xuan Du / Hongmiao Hu / Sisi Li / Xiaofeng Cao / Steven E Jacobsen / Jiamu Du / Abstract: In addition to the conserved RNA polymerases I to III (Pols I to III) in eukaryotes, two atypical polymerases, Pols IV and V, specifically produce noncoding RNA in the RNA-directed DNA methylation ...In addition to the conserved RNA polymerases I to III (Pols I to III) in eukaryotes, two atypical polymerases, Pols IV and V, specifically produce noncoding RNA in the RNA-directed DNA methylation pathway in plants. Here, we report on the structures of cauliflower Pol V in the free and elongation conformations. A conserved tyrosine residue of NRPE2 stacks with a double-stranded DNA branch of the transcription bubble to potentially attenuate elongation by inducing transcription stalling. The nontemplate DNA strand is captured by NRPE2 to enhance backtracking, thereby increasing 3'-5' cleavage, which likely underpins Pol V's high fidelity. The structures also illuminate the mechanism of Pol V transcription stalling and enhanced backtracking, which may be important for Pol V's retention on chromatin to serve its function in tethering downstream factors for RNA-directed DNA methylation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hil.cif.gz | 543.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hil.ent.gz | 425.9 KB | Display | PDB format |
PDBx/mmJSON format | 8hil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/8hil ftp://data.pdbj.org/pub/pdb/validation_reports/hi/8hil | HTTPS FTP |
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-Related structure data
Related structure data | 34820MC 8himC M: map data used to model this data C: citing same article (ref.) |
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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
-DNA-directed RNA polymerase ... , 2 types, 2 molecules AI
#1: Protein | Mass: 222800.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence |
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#7: Protein | Mass: 13123.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence / References: UniProt: A0A3P6GD79 |
-Protein , 4 types, 4 molecules BCKL
#2: Protein | Mass: 132377.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence |
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#3: Protein | Mass: 35484.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence / References: UniProt: A0A0D3D418 |
#9: Protein | Mass: 13538.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence / References: UniProt: A0A0D3DS91 |
#10: Protein | Mass: 5983.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence / References: UniProt: A0A0D2ZPP3 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 4 types, 4 molecules EFHJ
#4: Protein | Mass: 26260.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence / References: UniProt: A0A0D3DTU3 |
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#5: Protein | Mass: 16686.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence / References: UniProt: A0A0D3BZZ8 |
#6: Protein | Mass: 16607.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence / References: UniProt: A0A0D3DUD8 |
#8: Protein | Mass: 8167.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence / References: UniProt: A0A0D3AAT3 |
-Non-polymers , 2 types, 7 molecules
#11: Chemical | ChemComp-ZN / #12: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | Y |
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-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: DNA-directed RNA polymerase VPolymerase / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL |
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Source (natural) | Organism: Brassica oleracea (wild cabbage) / Tissue: inflorescence |
Buffer solution | pH: 7.8 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 280 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: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2.9975 sec. / Electron dose: 1.5625 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7068 |
-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 | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1609875 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63603 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||
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