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Yorodumi- EMDB-3729: RNA polymerase I pre-initiation complex (Pol-Rrn3 focused refinement) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3729 | |||||||||
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Title | RNA polymerase I pre-initiation complex (Pol-Rrn3 focused refinement) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.85 Å | |||||||||
Authors | Sadian Y / Tafur L / Kosinski J / Jakobi AJ / Wetzel R / Buczak K / Hagen WJH / Beck M / Sachse C / Muller CW | |||||||||
Citation | Journal: EMBO J / Year: 2017 Title: Structural insights into transcription initiation by yeast RNA polymerase I. Authors: Yashar Sadian / Lucas Tafur / Jan Kosinski / Arjen J Jakobi / Rene Wetzel / Katarzyna Buczak / Wim Jh Hagen / Martin Beck / Carsten Sachse / Christoph W Müller / Abstract: In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of ...In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi-subunit pre-initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo-EM structure of the 18-subunit yeast Pol I PIC bound to a transcription scaffold. The cryo-EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream DNA is positioned differently than in any previous structures of the Pol II PIC. Furthermore, the TFIIB-related subunit Rrn7 also occupies a different location compared to the Pol II PIC although it uses similar interfaces as TFIIB to contact DNA. Our results show that although general features of eukaryotic transcription initiation are conserved, Pol I and Pol II use them differently in their respective transcription initiation complexes. | |||||||||
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_3729.map.gz | 2.3 MB | EMDB map data format | |
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Header (meta data) | emd-3729-v30.xml emd-3729.xml | 22.8 KB 22.8 KB | Display Display | EMDB header |
Images | emd_3729.png | 111 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3729 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3729 | HTTPS FTP |
-Validation report
Summary document | emd_3729_validation.pdf.gz | 213 KB | Display | EMDB validaton report |
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Full document | emd_3729_full_validation.pdf.gz | 212.1 KB | Display | |
Data in XML | emd_3729_validation.xml.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3729 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3729 | HTTPS FTP |
-Related structure data
Related structure data | 3727C 3728C 5oa1FC F: fitted*YM C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3729.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...
+Supramolecule #1: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...
+Macromolecule #1: RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190
+Macromolecule #2: RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135
+Macromolecule #3: RPA49_YEAST DNA-directed RNA polymerase I subunit RPA49
+Macromolecule #4: RPA43_YEAST DNA-directed RNA polymerase I subunit RPA43
+Macromolecule #5: RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #6: RPA34_YEAST DNA-directed RNA polymerase I subunit RPA34
+Macromolecule #7: RPAB1_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #8: RPAB2_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #9: RPAC2_YEAST DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #10: RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #11: RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14
+Macromolecule #12: RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12
+Macromolecule #13: RPAB4_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #14: RPAB5_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #15: RRN3_YEAST RNA polymerase I-specific transcription initiation fac...
+Macromolecule #16: non-template DNA strand
+Macromolecule #17: template DNA strand
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 |
Grid | Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II |
-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 real images: 4235 / Average exposure time: 20.0 sec. / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 38589 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |