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Yorodumi- EMDB-34820: A cryo-EM structure of B. oleracea RNA polymerase V at 3.57 Angstrom -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34820 | |||||||||
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Title | A cryo-EM structure of B. oleracea RNA polymerase V at 3.57 Angstrom | |||||||||
Map data | ||||||||||
Sample |
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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) / wild cabbage (wild cabbage) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.57 Å | |||||||||
Authors | Du X / Xie G / Hu H / Du J | |||||||||
Funding support | 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34820.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-34820-v30.xml emd-34820.xml | 27.2 KB 27.2 KB | Display Display | EMDB header |
Images | emd_34820.png | 145.2 KB | ||
Others | emd_34820_half_map_1.map.gz emd_34820_half_map_2.map.gz | 80.7 MB 80.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34820 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34820 | HTTPS FTP |
-Related structure data
Related structure data | 8hilMC 8himC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34820.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.095 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34820_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34820_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : DNA-directed RNA polymerase V
+Supramolecule #1: DNA-directed RNA polymerase V
+Macromolecule #1: DNA-directed RNA polymerase V largest subunit
+Macromolecule #2: DNA-dependent RNA polymerase IV and V subunit 2
+Macromolecule #3: RPOLD domain-containing protein
+Macromolecule #4: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #7: DNA-directed RNA polymerase subunit
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #9: RNA_pol_L_2 domain-containing protein
+Macromolecule #10: DNA-directed RNA polymerases II, IV and V subunit 12
+Macromolecule #11: ZINC ION
+Macromolecule #12: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 8 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 7068 / Average exposure time: 2.9975 sec. / Average electron dose: 1.5625 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1609875 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2) |
Final reconstruction | Number classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 63603 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-8hil: |