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Yorodumi- PDB-5oqm: STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFII... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oqm | |||||||||||||||
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Title | STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR | |||||||||||||||
Components |
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Keywords | TRANSCRIPTION / transcription initiation / macromolecular complex | |||||||||||||||
Function / homology | Function and homology information meiotic gene conversion / 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 / TFIIH-class transcription factor complex binding / phosphatidylinositol-5-phosphate binding ...meiotic gene conversion / 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 / TFIIH-class transcription factor complex binding / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / core mediator complex / 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 / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / RPB4-RPB7 complex / DNA 5'-3' helicase / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / mediator complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIA complex / 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 / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA binding, bending / RNA Polymerase I Transcription Initiation / DNA duplex unwinding / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / 3'-5' DNA helicase activity / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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 / transcription factor TFIID complex / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / 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 I Promoter Escape / RNA polymerase II complex binding / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / TFIID-class transcription factor complex binding / nuclear-transcribed mRNA catabolic process / ATPase activator activity / transcription by RNA polymerase III / TFIIB-class transcription factor binding / RNA polymerase II activity / Dual incision in TC-NER / 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 / cellular response to nutrient levels / positive regulation of translational initiation / ATP-dependent activity, acting on DNA / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / translation initiation factor binding / TBP-class protein binding / DNA helicase activity / isomerase activity / DNA-templated transcription initiation / nucleotide-excision repair Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||||||||
Authors | Schilbach, S. / Hantsche, M. / Tegunov, D. / Dienemann, C. / Wigge, C. / Urlaub, H. / Cramer, P. | |||||||||||||||
Funding support | Germany, 4items
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Citation | Journal: Nature / Year: 2017 Title: Structures of transcription pre-initiation complex with TFIIH and Mediator. Authors: S Schilbach / M Hantsche / D Tegunov / C Dienemann / C Wigge / H Urlaub / P Cramer / Abstract: For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron ...For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II. | |||||||||||||||
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 | 5oqm.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5oqm.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 5oqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oqm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5oqm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5oqm_validation.xml.gz | 238.8 KB | Display | |
Data in CIF | 5oqm_validation.cif.gz | 385.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/5oqm ftp://data.pdbj.org/pub/pdb/validation_reports/oq/5oqm | HTTPS FTP |
-Related structure data
Related structure data | 3850MC 3846C 5oqjC 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
+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
+Transcription initiation factor ... , 6 types, 6 molecules MQRUVX
+DNA chain , 2 types, 2 molecules NT
+Protein , 3 types, 3 molecules OW3
+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/peptide , 1 types, 1 molecules Z
+Mediator of RNA polymerase II transcription subunit ... , 15 types, 15 molecules abcdefghijklmno
+Non-polymers , 3 types, 18 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 |
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Molecular weight | Value: 1.95 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.6 | ||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Specimen support | Details: QUANTIFOIL HOLEY GOLD GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF SAMPLE. Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE Details: Grids were blotted for 8 s and plunge-frozen in liquid ethane. |
-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: 105000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 13000 |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16000 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL |