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Yorodumi- PDB-8him: A cryo-EM structure of B. oleracea RNA polymerase V elongation co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8him | ||||||
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Title | A cryo-EM structure of B. oleracea RNA polymerase V elongation complex at 2.73 Angstrom | ||||||
Components |
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Keywords | TRANSCRIPTION / DNA-dependent RNA polymerase V | ||||||
Function / homology | Function and homology information : / 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 ...: / 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: 2.8 Å | ||||||
Authors | Hu, H. / Xie, G. / Du, X. / 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 | 8him.cif.gz | 564.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8him.ent.gz | 439.6 KB | Display | PDB format |
PDBx/mmJSON format | 8him.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/8him ftp://data.pdbj.org/pub/pdb/validation_reports/hi/8him | HTTPS FTP |
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-Related structure data
Related structure data | 34821MC 8hilC 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 chain , 2 types, 2 molecules TN
#1: DNA chain | Mass: 10482.763 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Brassica oleracea (wild cabbage) |
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#2: DNA chain | Mass: 10463.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Brassica oleracea (wild cabbage) |
-RNA chain , 1 types, 1 molecules P
#3: RNA chain | Mass: 6414.902 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Brassica oleracea (wild cabbage) |
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-DNA-directed RNA polymerase ... , 3 types, 3 molecules AIB
#4: Protein | Mass: 222876.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence |
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#11: 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 |
#13: Protein | Mass: 132377.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence |
-Protein , 3 types, 3 molecules CKL
#5: 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 |
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#8: 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 |
#9: 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 FJHE
#6: 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 |
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#7: Protein | Mass: 7982.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence / References: UniProt: A0A0D3AAT3 |
#10: 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 |
#12: Protein | Mass: 26260.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / Tissue: inflorescence |
-Non-polymers , 2 types, 7 molecules
#14: Chemical | ChemComp-MG / |
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#15: Chemical | ChemComp-ZN / |
-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 |
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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: 5694 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2750896 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 503124 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL |