+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3727 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | RNA polymerase I pre-initiation complex | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
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) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3727.map.gz | 3.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3727-v30.xml emd-3727.xml | 33.2 KB 33.2 KB | Display Display | EMDB header |
Images | emd_3727.png | 194.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3727 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3727 | HTTPS FTP |
-Validation report
Summary document | emd_3727_validation.pdf.gz | 213.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3727_full_validation.pdf.gz | 212.6 KB | Display | |
Data in XML | emd_3727_validation.xml.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3727 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3727 | HTTPS FTP |
-Related structure data
Related structure data | 5oa1MC 3728C 3729C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_3727.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-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...
+Supramolecule #2: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...
+Supramolecule #3: 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
+Macromolecule #4: RPA43_YEAST DNA-directed RNA polymerase I subunit
+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: RRN6_YEAST RNA polymerase I-specific transcription initiation fac...
+Macromolecule #17: RRN7_YEAST RNA polymerase I-specific transcription initiation fac...
+Macromolecule #18: RRN11_YEAST RNA polymerase I-specific transcription initiation fa...
+Macromolecule #19: non-template DNA strand
+Macromolecule #20: template DNA strand
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
---|---|
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 |
---|---|
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) |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 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 |