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Yorodumi- EMDB-2786: Architecture of the RNA polymerase II-Mediator core transcription... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2786 | |||||||||
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Title | Architecture of the RNA polymerase II-Mediator core transcription initiation complex | |||||||||
Map data | cITC-cMed | |||||||||
Sample |
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Keywords | transcription / transcription initiation / RNA polymerase II / General Transcription Factors / Mediator | |||||||||
Function / homology | Function and homology information meiotic gene conversion / 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 / core mediator complex / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding ...meiotic gene conversion / 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 / core mediator complex / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / 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 / RPB4-RPB7 complex / transcription factor TFIIF complex / mediator complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription preinitiation complex / DNA binding, bending / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / 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 / 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 polymerase II general transcription initiation factor activity / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / TFIID-class transcription factor complex binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription by RNA polymerase III / TFIIB-class transcription factor binding / nuclear-transcribed mRNA catabolic process / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / 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 activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / translesion synthesis / cellular response to nutrient levels / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / 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 / transcription corepressor activity / disordered domain specific binding / peroxisome / ribosome biogenesis / single-stranded DNA binding / protein-macromolecule adaptor activity / cellular response to heat / DNA-binding transcription factor binding / DNA recombination / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / nucleic acid binding / transcription coactivator activity / single-stranded RNA binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces mikatae (yeast) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.7 Å | |||||||||
Authors | Plaschka C / Lariviere L / Wenzeck L / Hemann M / Tegunov D / Petrotchenko EV / Borchers CH / 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2786.map.gz | 77.9 MB | EMDB map data format | |
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Header (meta data) | emd-2786-v30.xml emd-2786.xml | 40.6 KB 40.6 KB | Display Display | EMDB header |
Images | emd_2786.png | 97.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2786 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2786 | HTTPS FTP |
-Validation report
Summary document | emd_2786_validation.pdf.gz | 235.5 KB | Display | EMDB validaton report |
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Full document | emd_2786_full_validation.pdf.gz | 234.5 KB | Display | |
Data in XML | emd_2786_validation.xml.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2786 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2786 | HTTPS FTP |
-Related structure data
Related structure data | 4v1oMC 2784C 2785C 4v1mC 4v1nC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2786.map.gz / Format: CCP4 / Size: 81.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cITC-cMed | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : cITC-cMed
+Supramolecule #1000: cITC-cMed
+Macromolecule #1: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
+Macromolecule #2: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
+Macromolecule #3: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
+Macromolecule #4: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
+Macromolecule #5: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
+Macromolecule #6: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
+Macromolecule #7: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
+Macromolecule #8: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
+Macromolecule #9: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
+Macromolecule #10: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
+Macromolecule #11: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
+Macromolecule #12: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
+Macromolecule #13: TRANSCRIPTION INITIATION FACTOR IIB
+Macromolecule #14: TATA-box-binding protein
+Macromolecule #15: Transcription initiation factor IIF subunit alpha
+Macromolecule #16: Transcription initiation factor IIF subunit beta
+Macromolecule #17: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #18: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #19: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #20: Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #21: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #22: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #23: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #24: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #25: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #26: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #27: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #28: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #29: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #30: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #31: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #32: template DNA
+Macromolecule #33: nontemplate DNA
+Macromolecule #34: RNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 7.5 Details: 25 mM HEPES-KOH pH 7.5, 180 mM Potassium acetate, 5 % Glycerol, 5 mM DTT |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER Method: 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 then vitrified. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 2972 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 37169 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 37000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Particles were picked using EMAN2 and were processed using RELION 1.2. |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: OTHER / Software - Name: RELION, 1.2 Details: The density was filtered according to local resolution and further a temperature factor of minus 340 A2 was applied. Number images used: 3267 |