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Yorodumi- PDB-8ceo: Yeast RNA polymerase II transcription pre-initiation complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ceo | |||||||||
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Title | Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome | |||||||||
Components |
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Keywords | TRANSCRIPTION / PIC / Mediator / nucleosome / TF | |||||||||
Function / homology | Function and homology information : / regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / positive regulation of mitotic recombination / core mediator complex / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / negative regulation of ribosomal protein gene transcription by RNA polymerase II ...: / regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / positive regulation of mitotic recombination / core mediator complex / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II core complex assembly / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / mediator complex / transcription factor TFIIA complex / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA duplex unwinding / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / 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 / 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 / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / nucleolar large rRNA transcription by RNA polymerase I / 3'-5' DNA helicase activity / 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 / nuclear-transcribed mRNA catabolic process / Estrogen-dependent gene expression / TFIID-class transcription factor complex binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / ATPase activator activity / transcription by RNA polymerase III / acetyltransferase activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / RNA polymerase II activity / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / tRNA transcription by RNA polymerase III / 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 I activity / RNA polymerase II, core complex / translesion synthesis / RNA polymerase II preinitiation complex assembly / DNA helicase activity / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / positive regulation of 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 / structural constituent of chromatin / nucleosome / ribosome biogenesis / nucleosome assembly / peroxisome / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Xenopus laevis (African clawed frog) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wang, H. / Cramer, P. | |||||||||
Funding support | European Union, Germany, 2items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Yeast PIC-Mediator structure with RNA polymerase II C-terminal domain. Authors: Sandra Schilbach / Haibo Wang / Christian Dienemann / Patrick Cramer / Abstract: For transcription initiation, RNA polymerase II (Pol II) forms a preinitiation complex (PIC) that associates with the general coactivator Mediator. Whereas atomic models of the human PIC-Mediator ...For transcription initiation, RNA polymerase II (Pol II) forms a preinitiation complex (PIC) that associates with the general coactivator Mediator. Whereas atomic models of the human PIC-Mediator structure have been reported, structures for its yeast counterpart remain incomplete. Here, we present an atomic model for the yeast PIC with core Mediator, including the Mediator middle module that was previously poorly resolved and including subunit Med1 that was previously lacking. We observe three peptide regions containing eleven of the 26 heptapeptide repeats of the flexible C-terminal repeat domain (CTD) of Pol II. Two of these CTD regions bind between the Mediator head and middle modules and form defined CTD-Mediator interactions. CTD peptide 1 binds between the Med6 shoulder and Med31 knob domains, whereas CTD peptide 2 forms additional contacts with Med4. The third CTD region (peptide 3) binds in the Mediator cradle and associates with the Mediator hook. Comparisons with the human PIC-Mediator structure show that the central region in peptide 1 is similar and forms conserved contacts with Mediator, whereas peptides 2 and 3 exhibit distinct structures and Mediator interactions. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ceo.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ceo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ceo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/8ceo ftp://data.pdbj.org/pub/pdb/validation_reports/ce/8ceo | HTTPS FTP |
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-Related structure data
Related structure data | 16611MC 8cenC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
+Protein , 8 types, 12 molecules 16OUrvswtxuy
+RNA polymerase II transcription factor B subunit ... , 2 types, 2 molecules 23
+General transcription and DNA repair factor IIH subunit ... , 2 types, 2 molecules 45
+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 MQRVWX
+DNA chain , 2 types, 2 molecules NT
+Mediator of RNA polymerase II transcription subunit ... , 16 types, 16 molecules abcdefghijklmnop
+Non-polymers , 3 types, 19 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 core Mediator and the +1 nucleosome Type: COMPLEX / Entity ID: #1-#50 / Source: RECOMBINANT |
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Molecular weight | Value: 2.2 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: 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 defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50715 / Symmetry type: POINT | ||||||||||||||||||||||||
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