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Yorodumi- PDB-7o72: Yeast RNA polymerase II transcription pre-initiation complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o72 | ||||||||||||||||||
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Title | Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA | ||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / Pre-initiation complex | ||||||||||||||||||
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 transcription by RNA polymerase III ...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 / 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 / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / DNA 5'-3' helicase / transcription factor TFIIF complex / transcription factor TFIIA complex / phosphatidylinositol-3-phosphate binding / RNA polymerase I preinitiation complex assembly / 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 / DNA binding, bending / 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 / transcription factor TFIID complex / termination of RNA polymerase II transcription / 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 / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / RNA Polymerase I Promoter Escape / protein phosphatase activator activity / 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 / RNA polymerase II activity / Dual incision in TC-NER / transcription-coupled nucleotide-excision repair / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / 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 / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA helicase activity / isomerase activity / DNA-templated transcription initiation / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / transcription coregulator activity / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||
Authors | Schilbach, S. / Aibara, S. / Dienemann, C. / Grabbe, F. / Cramer, P. | ||||||||||||||||||
Funding support | Germany, 5items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7o72.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7o72.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 7o72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o72_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7o72_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7o72_validation.xml.gz | 215.8 KB | Display | |
Data in CIF | 7o72_validation.cif.gz | 336.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/7o72 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/7o72 | HTTPS FTP |
-Related structure data
Related structure data | 12743MC 7o4iC 7o4jC 7o4kC 7o4lC 7o73C 7o75C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+General transcription and DNA repair factor IIH helicase subunit ... , 2 types, 2 molecules 07
+General transcription and DNA repair factor IIH subunit ... , 5 types, 5 molecules 12456
+Protein , 3 types, 3 molecules 3MO
+DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK
+DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
+DNA chain , 2 types, 2 molecules NT
+Transcription initiation factor IIF subunit ... , 2 types, 2 molecules QR
+Transcription initiation factor IIA ... , 2 types, 2 molecules UV
+Transcription initiation factor IIE subunit ... , 2 types, 2 molecules WX
+Non-polymers , 5 types, 22 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Type: COMPLEX / Entity ID: #1-#30 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 1.37 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R3.5/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 9 sec. / Electron dose: 43.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 29670 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4300000 | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11014 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | |||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5OQJ Accession code: 5OQJ / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 125.03 Å2 | |||||||||||||||||||||||||||
Refine LS restraints |
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