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Yorodumi- EMDB-12744: Yeast RNA polymerase II transcription pre-initiation complex with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12744 | ||||||||||||||||||
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Title | Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA | ||||||||||||||||||
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Sample |
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Function / homology | Function and homology information : / regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination ...: / regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / DNA translocase activity / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / phosphatidylinositol-3-phosphate binding / 5'-3' DNA helicase activity / transcription factor TFIIA complex / : / RNA polymerase I preinitiation complex assembly / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 3'-5' DNA helicase activity / transcription preinitiation complex / poly(A)+ mRNA export from nucleus / DNA binding, bending / RNA Polymerase I Transcription Initiation / DNA duplex unwinding / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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 polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase II complex binding / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / ATPase activator activity / protein phosphatase activator activity / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / positive regulation of transcription initiation by RNA polymerase II / translesion synthesis / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / ATP-dependent activity, acting on DNA / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / RNA polymerase II preinitiation complex assembly / DNA helicase activity / TBP-class protein binding / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (brewer's yeast) / synthetic construct (others) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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
-Related structure data
Related structure data | 7o73MC 7o4iC 7o4jC 7o4kC 7o4lC 7o72C 7o75C 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_12744.map.gz / Format: CCP4 / Size: 209.3 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
+Additional map: Locally filtered map (non-composite) of a CC-dist refinement...
+Additional map: Half-map 2 of focused refinement encompassing the Ssl1/Tfb4/Tfb1-3-helix-bundle...
+Additional map: Half-map 1 of focused refinement encompassing the Ssl1/Tfb4/Tfb1-3-helix-bundle...
+Additional map: Half-map 2 of focused refinement encompassing the Rad3/Ssl1...
+Additional map: Half-map 1 of focused refinement encompassing the Rad3/Ssl1...
+Additional map: Half-map 1 of focused refinement encompassing the Ssl2/Tfb2/Tfb5...
+Additional map: Half-map 2 of focused refinement encompassing the Pol...
+Additional map: Half-map 2 of focused refinement encompassing the Ssl2/Tfb2/Tfb5...
+Additional map: Half-map 1 of focused refinement encompassing the Pol...
+Additional map: Half-map 2 of focused refinement encompassing the Tfb2...
+Additional map: Half-map 1 of focused refinement encompassing the Pol...
+Additional map: Half-map 2 of focused refinement encompassing the Pol...
+Additional map: Half-map 2 of focused refinement encompassing the Pol...
+Additional map: Half-map 1 of focused refinement encompassing the Tfb2...
+Additional map: Half-map 2 of focused refinement encompassing the Pol...
+Additional map: Half-map 1 of focused refinement encompassing the Pol...
+Additional map: Half-map 1 of focused refinement encompassing the Pol...
+Additional map: Half-map 2 of focused refinement encompassing the Pol...
+Additional map: Half-map 1 of focused refinement encompassing the Pol...
+Additional map: Half-map 1 of focused refinement encompassing the Pol...
+Additional map: Half-map 2 of focused refinement encompassing the Pol...
+Half map: #2
+Half map: #1
-Sample components
+Entire : Yeast RNA polymerase II transcription pre-initiation complex with...
+Supramolecule #1: Yeast RNA polymerase II transcription pre-initiation complex with...
+Macromolecule #1: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #2: General transcription and DNA repair factor IIH subunit TFB1
+Macromolecule #3: General transcription and DNA repair factor IIH subunit TFB2
+Macromolecule #4: RNA polymerase II transcription factor B subunit 3
+Macromolecule #5: General transcription and DNA repair factor IIH subunit TFB4
+Macromolecule #6: General transcription and DNA repair factor IIH subunit TFB5
+Macromolecule #7: General transcription and DNA repair factor IIH subunit SSL1
+Macromolecule #8: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #10: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #12: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #13: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #14: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #15: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #16: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #17: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #18: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #19: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #20: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #21: Transcription initiation factor IIB
+Macromolecule #23: TATA-box-binding protein
+Macromolecule #24: Transcription initiation factor IIF subunit alpha
+Macromolecule #25: Transcription initiation factor IIF subunit beta
+Macromolecule #27: Transcription initiation factor IIA large subunit
+Macromolecule #28: Transcription initiation factor IIA subunit 2
+Macromolecule #29: Transcription initiation factor IIE subunit alpha
+Macromolecule #30: Transcription initiation factor IIE subunit beta
+Macromolecule #22: Non-template DNA
+Macromolecule #26: Template DNA
+Macromolecule #31: IRON/SULFUR CLUSTER
+Macromolecule #32: ZINC ION
+Macromolecule #33: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #34: MAGNESIUM ION
+Macromolecule #35: ADENOSINE-5'-DIPHOSPHATE
-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 |