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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 / DNA translocase activity / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / 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 / DNA translocase activity / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / 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 / mediator complex / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / 5'-3' DNA helicase activity / transcription factor TFIIA complex / : / 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 / 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 general transcription initiation factor activity / 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 / 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 / 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 / TFIID-class transcription factor complex binding / 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 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 / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / DNA-templated transcription initiation / 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 / cytoplasmic stress granule / peroxisome / structural constituent of chromatin / nucleosome / single-stranded DNA binding / ribosome biogenesis / 4 iron, 4 sulfur cluster binding / DNA helicase / transcription by RNA polymerase II / damaged DNA binding / single-stranded RNA binding / nucleic acid binding 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 FIELDBright-field microscopy / 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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