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Yorodumi- EMDB-10544: early intermediate RNA Polymerase I Pre-initiation complex - eiPIC -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10544 | |||||||||
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Title | early intermediate RNA Polymerase I Pre-initiation complex - eiPIC | |||||||||
Map data | eiPIC reconstruction postprocessed | |||||||||
Sample |
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Keywords | Transcription Initiation / Ribosome Biosynthesis / RNA Polymerase I / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I core binding / rDNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA ...RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I core binding / rDNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / regulation of cell size / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase III activity / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.54 Å | |||||||||
Authors | Pilsl M / Engel C | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis of RNA polymerase I pre-initiation complex formation and promoter melting. Authors: Michael Pilsl / Christoph Engel / Abstract: Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a prerequisite for the biosynthesis of ribosomes in eukaryotes. Compared to Pols II and III, the mechanisms underlying ...Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a prerequisite for the biosynthesis of ribosomes in eukaryotes. Compared to Pols II and III, the mechanisms underlying promoter recognition, initiation complex formation and DNA melting by Pol I substantially diverge. Here, we report the high-resolution cryo-EM reconstruction of a Pol I early initiation intermediate assembled on a double-stranded promoter scaffold that prevents the establishment of downstream DNA contacts. Our analyses demonstrate how efficient promoter-backbone interaction is achieved by combined re-arrangements of flexible regions in the 'core factor' subunits Rrn7 and Rrn11. Furthermore, structure-function analysis illustrates how destabilization of the melted DNA region correlates with contraction of the polymerase cleft upon transcription activation, thereby combining promoter recruitment with DNA-melting. This suggests that molecular mechanisms and structural features of Pol I initiation have co-evolved to support the efficient melting, initial transcription and promoter clearance required for high-level rRNA synthesis. | |||||||||
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_10544.map.gz | 263.1 MB | EMDB map data format | |
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Header (meta data) | emd-10544-v30.xml emd-10544.xml | 44.7 KB 44.7 KB | Display Display | EMDB header |
Images | emd_10544.png | 227.1 KB | ||
Filedesc metadata | emd-10544.cif.gz | 11.9 KB | ||
Others | emd_10544_additional.map.gz | 258.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10544 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10544 | HTTPS FTP |
-Validation report
Summary document | emd_10544_validation.pdf.gz | 625.1 KB | Display | EMDB validaton report |
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Full document | emd_10544_full_validation.pdf.gz | 624.6 KB | Display | |
Data in XML | emd_10544_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_10544_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10544 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10544 | HTTPS FTP |
-Related structure data
Related structure data | 6tpsMC 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_10544.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | eiPIC reconstruction postprocessed | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: focused CF refinement postporocessed
File | emd_10544_additional.map | ||||||||||||
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Annotation | focused CF refinement postporocessed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : early intermediate RNA-Polymerase I Pre-initiation Complex - eiPIC
+Supramolecule #1: early intermediate RNA-Polymerase I Pre-initiation Complex - eiPIC
+Supramolecule #2: RNA polymerase
+Supramolecule #3: transcription initiation factor
+Supramolecule #4: DNA
+Macromolecule #1: DNA-directed RNA polymerase I subunit RPA190
+Macromolecule #2: DNA-directed RNA polymerase I subunit RPA135
+Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #4: DNA-directed RNA polymerase I subunit RPA14
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #7: DNA-directed RNA polymerase I subunit RPA43
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase I subunit RPA12
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #13: DNA-directed RNA polymerase I subunit RPA49
+Macromolecule #14: DNA-directed RNA polymerase I subunit RPA34
+Macromolecule #15: RNA polymerase I-specific transcription initiation factor RRN3
+Macromolecule #16: RNA polymerase I-specific transcription initiation factor RRN6
+Macromolecule #17: RNA polymerase I-specific transcription initiation factor RRN7
+Macromolecule #18: RNA polymerase I-specific transcription initiation factor RRN11
+Macromolecule #19: NTS-DNA (27-MER)
+Macromolecule #20: TS-DNA (27-MER)
+Macromolecule #21: DNA foreign
+Macromolecule #22: DNA foreign
+Macromolecule #23: ZINC ION
+Macromolecule #24: 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 / Component - Formula: KCl |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 4088 / Average electron dose: 1.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE / Details: Initial model generated from 2D classes |
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Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 122099 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION / Software - details: 3 |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION / Software - details: 3 |