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- EMDB-34820: A cryo-EM structure of B. oleracea RNA polymerase V at 3.57 Angstrom -
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Open data
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Basic information
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Title | A cryo-EM structure of B. oleracea RNA polymerase V at 3.57 Angstrom | |||||||||
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![]() | DNA-dependent RNA polymerase V / TRANSCRIPTION | |||||||||
Function / homology | ![]() RNA polymerase IV complex / RNA polymerase V complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity ...RNA polymerase IV complex / RNA polymerase V complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II activity / transcription initiation at RNA polymerase II promoter / 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.57 Å | |||||||||
![]() | Du X / Xie G / Hu H / Du J | |||||||||
Funding support | 1 items
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![]() | ![]() 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 | ![]() | 7.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.8 KB 27.8 KB | Display Display | ![]() |
Images | ![]() | 145.2 KB | ||
Filedesc metadata | ![]() | 8.6 KB | ||
Others | ![]() ![]() | 80.7 MB 80.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 801.2 KB | Display | ![]() |
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Full document | ![]() | 800.8 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hilMC ![]() 8himC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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 |
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | ![]() PDB-8hil: |