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Yorodumi- PDB-4v1n: Architecture of the RNA polymerase II-Mediator core transcription... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v1n | |||||||||
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Title | Architecture of the RNA polymerase II-Mediator core transcription initiation complex | |||||||||
Components |
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Keywords | TRANSCRIPTION / TRANSCRIPTION INITIATION / RNA POLYMERASE II / GENERAL TRANSCRIPTION FACTORS | |||||||||
Function / homology | Function and homology information RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase I general transcription initiation factor binding / transcription open complex formation at RNA polymerase II promoter / regulation of transcription by RNA polymerase III / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex ...RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase I general transcription initiation factor binding / transcription open complex formation at RNA polymerase II promoter / regulation of transcription by RNA polymerase III / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / RNA polymerase II core complex assembly / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / DNA binding, bending / 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 / TP53 Regulates Transcription of DNA Repair Genes / 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 / termination of RNA polymerase II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / 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 / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / acetyltransferase activity / transcription factor TFIID complex / Dual incision in TC-NER / RNA polymerase II general transcription initiation factor activity / transcription elongation by RNA polymerase I / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / peroxisome / disordered domain specific binding / ribosome biogenesis / single-stranded DNA binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm Similarity search - Function | |||||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) SACCHAROMYCES MIKATAE (yeast) SYNTHETIC CONSTRUCT (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å | |||||||||
Authors | Plaschka, C. / Lariviere, L. / Wenzeck, L. / Hemann, M. / Tegunov, D. / Petrotchenko, E.V. / Borchers, C.H. / Baumeister, W. / Herzog, F. / Villa, E. / Cramer, P. | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Architecture of the RNA polymerase II-Mediator core initiation complex. Authors: C Plaschka / L Larivière / L Wenzeck / M Seizl / M Hemann / D Tegunov / E V Petrotchenko / C H Borchers / W Baumeister / F Herzog / E Villa / P Cramer / Abstract: The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all ...The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 Å resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation. | |||||||||
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 | 4v1n.cif.gz | 1009.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v1n.ent.gz | 779.7 KB | Display | PDB format |
PDBx/mmJSON format | 4v1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v1n_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4v1n_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4v1n_validation.xml.gz | 133.9 KB | Display | |
Data in CIF | 4v1n_validation.cif.gz | 204.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/4v1n ftp://data.pdbj.org/pub/pdb/validation_reports/v1/4v1n | HTTPS FTP |
-Related structure data
Related structure data | 2785MC 2784C 2786C 4v1mC 4v1oC C: citing same article (ref.) M: map data used to model this data |
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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
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P04050, DNA-directed RNA polymerase |
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#2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P08518, DNA-directed RNA polymerase |
#3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P16370 |
#4: Protein | Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20433 |
#7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P34087 |
#9: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P27999 |
#11: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Fragment: 2.7.7.6 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P38902 |
-DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ... , 5 types, 5 molecules EFHJL
#5: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20434 |
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#6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20435 |
#8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20436 |
#10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P22139 |
#12: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P40422 |
-Protein , 2 types, 2 molecules MO
#13: Protein | Mass: 38257.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29055 |
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#15: Protein | Mass: 20251.949 Da / Num. of mol.: 1 / Fragment: RESIDUES 61-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P13393 |
-DNA chain , 2 types, 2 molecules NT
#14: DNA chain | Mass: 15449.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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#19: DNA chain | Mass: 17812.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-RNA chain , 1 types, 1 molecules P
#16: RNA chain | Mass: 1860.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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-TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ... , 2 types, 2 molecules QR
#17: Protein | Mass: 82366.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES MIKATAE (yeast) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29055, UniProt: A0A0H2UKZ8*PLUS |
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#18: Protein | Mass: 37918.438 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-140,210-400 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P41896, DNA helicase |
-Non-polymers , 2 types, 10 molecules
#20: Chemical | ChemComp-ZN / #21: Chemical | ChemComp-MG / | |
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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: CITC / Type: COMPLEX |
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Buffer solution | Name: 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT pH: 7.5 Details: 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT |
Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Cryogen name: ETHANE Details: GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY ...Details: GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Aug 1, 2013 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 37000 X / Calibrated magnification: 37169 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
-Processing
EM software | Name: RELION / Version: 1.2 / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: EACH PARTICLE | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 7.8 Å / Num. of particles: 4439 / Nominal pixel size: 1.35 Å / Actual pixel size: 1.35 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2785. Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY | ||||||||||||
Refinement | Highest resolution: 7.8 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7.8 Å
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