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Yorodumi- EMDB-31305: The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31305 | |||||||||
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Title | The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA-directed RNA polymerase IV / RNA- dependent RNA polymerase 2 / RNA-directed DNA methylation pathway / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information RNA polymerase IV complex / stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / retrotransposon silencing by siRNA-directed DNA methylation / RNA polymerase V complex / stomatal complex development / siRNA transcription / DNA/RNA hybrid binding / : / regulatory ncRNA-mediated post-transcriptional gene silencing ...RNA polymerase IV complex / stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / retrotransposon silencing by siRNA-directed DNA methylation / RNA polymerase V complex / stomatal complex development / siRNA transcription / DNA/RNA hybrid binding / : / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / regulatory ncRNA-mediated gene silencing / RNA polymerase complex / regulation of immune response / RNA polymerase III activity / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / defense response to fungus / heterochromatin / RNA polymerase II activity / RNA polymerase II, core complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / DNA-templated transcription / nucleolus / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
Authors | Fang CL / Wu XX | |||||||||
Funding support | China, 1 items
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Citation | Journal: Science / Year: 2021 Title: Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA. Authors: Kun Huang / Xiao-Xian Wu / Cheng-Li Fang / Zhou-Geng Xu / Hong-Wei Zhang / Jian Gao / Chuan-Miao Zhou / Lin-Lin You / Zhan-Xi Gu / Wen-Hui Mu / Yu Feng / Jia-Wei Wang / Yu Zhang / Abstract: DNA methylation affects gene expression and maintains genome integrity. The DNA-dependent RNA polymerase IV (Pol IV), together with the RNA-dependent RNA polymerase RDR2, produces double-stranded ...DNA methylation affects gene expression and maintains genome integrity. The DNA-dependent RNA polymerase IV (Pol IV), together with the RNA-dependent RNA polymerase RDR2, produces double-stranded small interfering RNA precursors essential for establishing and maintaining DNA methylation in plants. We determined the cryo–electron microscopy structures of the Pol IV–RDR2 holoenzyme and the backtracked transcription elongation complex. These structures reveal that Pol IV and RDR2 form a complex with their active sites connected by an interpolymerase channel, through which the Pol IV–generated transcript is handed over to the RDR2 active site after being backtracked, where it is used as the template for double-stranded RNA (dsRNA) synthesis. Our results describe a ‘backtracking-triggered RNA channeling’ mechanism underlying dsRNA synthesis and also shed light on the evolutionary trajectory of eukaryotic RNA polymerases. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31305.map.gz | 9.8 MB | EMDB map data format | |
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Header (meta data) | emd-31305-v30.xml emd-31305.xml | 35.5 KB 35.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31305_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_31305.png | 113.8 KB | ||
Filedesc metadata | emd-31305.cif.gz | 9.9 KB | ||
Others | emd_31305_additional_1.map.gz emd_31305_half_map_1.map.gz emd_31305_half_map_2.map.gz | 65.3 MB 65.5 MB 65.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31305 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31305 | HTTPS FTP |
-Related structure data
Related structure data | 7eu0MC 7eu1C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31305.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_31305_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31305_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31305_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : A. thaliana Pol IV-RDR2 backtracked complex
+Supramolecule #1: A. thaliana Pol IV-RDR2 backtracked complex
+Macromolecule #1: DNA-directed RNA polymerase IV subunit 1
+Macromolecule #2: DNA-directed RNA polymerases IV and V subunit 2
+Macromolecule #3: DNA-directed RNA polymerases II, IV and V subunit 3
+Macromolecule #4: DNA-directed RNA polymerases II and IV subunit 5A
+Macromolecule #5: DNA-directed RNA polymerases II, IV and V subunit 6A
+Macromolecule #6: DNA-directed RNA polymerases II, IV and V subunit 8B
+Macromolecule #7: DNA-directed RNA polymerases II, IV and V subunit 9A
+Macromolecule #8: DNA-directed RNA polymerases II, IV and V subunit 10
+Macromolecule #9: DNA-directed RNA polymerases II, IV and V subunit 11
+Macromolecule #10: DNA-directed RNA polymerases II, IV and V subunit 12
+Macromolecule #11: RNA-dependent RNA polymerase 2
+Macromolecule #12: DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*GP*AP*GP*...
+Macromolecule #14: DNA (33-MER)
+Macromolecule #13: RNA (39-MER)
+Macromolecule #15: RNA (5'-R(*CP*CP*GP*A)-3')
+Macromolecule #16: ZINC ION
+Macromolecule #17: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.1 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 120 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 282.65 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Average electron dose: 1.95 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |