+Open data
-Basic information
Entry | Database: PDB / ID: 7uig | ||||||
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Title | Mediator-PIC Early (Mediator A) | ||||||
Components |
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Keywords | TRANSCRIPTION / Divergent transcription / Mediator / RNA Polymerase II / PIC / Pre-Initiation / Activation / Transcription Factor / Gal4 / Gal4VP16 | ||||||
Function / homology | Function and homology information meiotic gene conversion / RNA polymerase II complex recruiting activity / TFIIH-class transcription factor complex binding / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / mediator complex / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex ...meiotic gene conversion / RNA polymerase II complex recruiting activity / TFIIH-class transcription factor complex binding / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / mediator complex / Processing of Capped Intron-Containing Pre-mRNA / 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 / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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 / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TFIID-class transcription factor complex binding / TFIIB-class transcription factor binding / positive regulation of transcription initiation by RNA polymerase II / translesion synthesis / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / transcription corepressor activity / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / DNA recombination / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA repair / regulation of transcription by RNA polymerase II / structural molecule activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Gorbea Colon, J.J. / Chen, S.-F. / Tsai, K.L. / Murakami, K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol Cell / Year: 2023 Title: Structural basis of a transcription pre-initiation complex on a divergent promoter. Authors: Jose J Gorbea Colón / Leon Palao / Shin-Fu Chen / Hee Jong Kim / Laura Snyder / Yi-Wei Chang / Kuang-Lei Tsai / Kenji Murakami / Abstract: Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single ...Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uig.cif.gz | 674.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uig.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7uig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/7uig ftp://data.pdbj.org/pub/pdb/validation_reports/ui/7uig | HTTPS FTP |
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-Related structure data
Related structure data | 26545MC 7ui9C 7uicC 7uifC 7uikC 7uilC 7uioC 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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-Components
-Mediator of RNA polymerase II transcription subunit ... , 16 types, 16 molecules adfghijknqrstuvw
#1: Protein | Mass: 64314.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12321 |
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#2: Protein | Mass: 32244.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12343 |
#3: Protein | Mass: 32844.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38782 |
#4: Protein | Mass: 25616.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q08278 |
#5: Protein | Mass: 25297.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38304 |
#6: Protein | Mass: 17400.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33308 |
#7: Protein | Mass: 17927.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q06213 |
#8: Protein | Mass: 13324.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q99278 |
#9: Protein | Mass: 123500.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P19263 |
#10: Protein | Mass: 78582.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32569 |
#11: Protein | Mass: 34316.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32585 |
#12: Protein | Mass: 24885.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P25046 |
#13: Protein | Mass: 22918.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P34162 |
#14: Protein | Mass: 16093.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P47822 |
#15: Protein | Mass: 13875.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32570 |
#16: Protein | Mass: 14747.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38633 |
-Protein , 1 types, 1 molecules z
#17: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P04050, DNA-directed RNA polymerase |
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-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: Core Mediator-PICearly (Copy A) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||
Buffer solution | pH: 7.6 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM CPC / 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 magnification: 64000 X / Calibrated magnification: 64000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.4 sec. / Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 40900 |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 341314 / Symmetry type: POINT |