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Yorodumi- EMDB-12722: Yeast TFIIH in the expanded state within the pre-initiation complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12722 | ||||||||||||||||||
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Title | Yeast TFIIH in the expanded state within the pre-initiation complex | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | Pre-initiation complex / TRANSCRIPTION | ||||||||||||||||||
Function / homology | Function and homology information regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter ...regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / DNA 5'-3' helicase / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / DNA duplex unwinding / poly(A)+ mRNA export from nucleus / 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 / 3'-5' DNA helicase activity / 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 / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / ATPase activator activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Estrogen-dependent gene expression / nuclear-transcribed mRNA catabolic process / 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 / ATP-dependent activity, acting on DNA / positive regulation of translational initiation / translesion synthesis / RNA polymerase II, core complex / translation initiation factor binding / DNA helicase activity / isomerase activity / DNA-templated transcription initiation / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing / ubiquitin protein ligase activity / ribosome biogenesis / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / double-stranded DNA binding / transcription by RNA polymerase II / damaged DNA binding / single-stranded RNA binding / DNA repair / nucleotide binding / mRNA binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||
Authors | Schilbach S / Aibara S | ||||||||||||||||||
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
-Validation report
Summary document | emd_12722_validation.pdf.gz | 718.4 KB | Display | EMDB validaton report |
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Full document | emd_12722_full_validation.pdf.gz | 718 KB | Display | |
Data in XML | emd_12722_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | emd_12722_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12722 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12722 | HTTPS FTP |
-Related structure data
Related structure data | 7o4lMC 7o4iC 7o4jC 7o4kC 7o72C 7o73C 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_12722.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 refinement of...
+Additional map: Half-map 2 of focused refinement encompassing the Ssl1/Tfb4-eZnF/Tfb1-3-helix-bundle...
+Additional map: Half-map 2 of focused refinement encompassing the Tfb2...
+Additional map: Half-map 2 of focused refinement encompassing the Ssl2/Tfb2/Tfb5...
+Additional map: Half-map 1 of focused refinement encompassing the Tfb2...
+Additional map: Half-map 1 of focused refinement encompassing the Tfb3-RING-finger/TFIIE/Pol...
+Additional map: Half-map 2 of focused refinement encompassing the Tfb3-RING-finger/TFIIE/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 2 of focused refinement encompassing the Rad3/Ssl1...
+Additional map: Half-map 2 of focused refinement encompassing the Pol...
+Additional map: Half-map 1 of focused refinement encompassing the Rad3/Ssl1...
+Additional map: Half-map 1 of focused refinement encompassing the Ssl1/Tfb4-eZnF/Tfb1-3-helix-bundle...
+Additional map: Half-map 1 of focused refinement encompassing the Ssl2/Tfb2/Tfb5...
+Half map: #2
+Half map: #1
-Sample components
+Entire : Yeast TFIIH in the expanded state within the pre-initiation complex
+Supramolecule #1: Yeast TFIIH in the expanded state within the pre-initiation complex
+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 RPB4
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #13: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #16: Transcription initiation factor IIE subunit alpha
+Macromolecule #17: Transcription initiation factor IIE subunit beta
+Macromolecule #14: Nontemplate DNA
+Macromolecule #15: Template DNA
+Macromolecule #18: IRON/SULFUR CLUSTER
+Macromolecule #19: ZINC ION
+Macromolecule #20: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #21: MAGNESIUM ION
+Macromolecule #22: 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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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
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 |
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: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |