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Yorodumi- EMDB-12725: Focused refinement of RNA polymerase II (10-subunit) - TFIIB regi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12725 | ||||||||||||||||||
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Title | Focused refinement of RNA polymerase II (10-subunit) - TFIIB region of a transcription pre-initiation assembly | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||||||||||||||
Authors | Schilbach S / Aibara S / Dienemann C / Grabbe F / Cramer P | ||||||||||||||||||
Funding support | Germany, 5 items
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Citation | Journal: Cell / Year: 2021 Title: Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening. Authors: Sandra Schilbach / Shintaro Aibara / Christian Dienemann / Frauke Grabbe / Patrick Cramer / Abstract: Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of ...Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of the yeast PIC and define the mechanism of initial DNA opening. We trap the PIC in an intermediate state that contains half a turn of open DNA located 30-35 base pairs downstream of the TATA box. The initially opened DNA region is flanked and stabilized by the polymerase "clamp head loop" and the TFIIF "charged region" that both contribute to promoter-initiated transcription. TFIIE facilitates initiation by buttressing the clamp head loop and by regulating the TFIIH translocase. The initial DNA bubble is then extended in the upstream direction, leading to the open promoter complex and enabling start-site scanning and RNA synthesis. This unique mechanism of DNA opening may permit more intricate regulation than in the Pol I and Pol III systems. | ||||||||||||||||||
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_12725.map.gz | 75.2 MB | EMDB map data format | |
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Header (meta data) | emd-12725-v30.xml emd-12725.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12725_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_12725.png | 66.5 KB | ||
Masks | emd_12725_msk_1.map | 83.7 MB | Mask map | |
Others | emd_12725_half_map_1.map.gz emd_12725_half_map_2.map.gz | 74.5 MB 74.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12725 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12725 | HTTPS FTP |
-Related structure data
Related structure data | 7o4iC 7o4jC 7o4kC 7o4lC 7o72C 7o73C 7o75C 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_12725.map.gz / Format: CCP4 / Size: 83.7 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: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12725_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12725_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12725_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Yeast RNA polymerase II transcription pre-initiation complex
Entire | Name: Yeast RNA polymerase II transcription pre-initiation complex |
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Components |
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-Supramolecule #1: Yeast RNA polymerase II transcription pre-initiation complex
Supramolecule | Name: Yeast RNA polymerase II transcription pre-initiation complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Theoretical: 1.37 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
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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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: 4.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 29670 / Average exposure time: 9.0 sec. / Average electron dose: 43.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |