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Yorodumi- EMDB-2784: Architecture of the RNA polymerase II-Mediator core transcription... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2784 | |||||||||
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Title | Architecture of the RNA polymerase II-Mediator core transcription initiation complex | |||||||||
Map data | Pol II-DNA/RNA | |||||||||
Sample |
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Keywords | transcription / transcription initiation / RNA polymerase II / General Transcription Factors | |||||||||
Function / homology | Function and homology information RPB4-RPB7 complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / : / 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 ...RPB4-RPB7 complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / : / 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 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 I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / 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 / positive regulation of translational initiation / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / transcription by RNA polymerase II / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 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_2784.map.gz | 77.8 MB | EMDB map data format | |
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Header (meta data) | emd-2784-v30.xml emd-2784.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
Images | emd_2784.png | 109.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2784 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2784 | HTTPS FTP |
-Related structure data
Related structure data | 4v1mMC 2785C 2786C 4v1nC 4v1oC 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_2784.map.gz / Format: CCP4 / Size: 81.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Pol II-DNA/RNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Pol II-DNA/RNA
+Supramolecule #1000: Pol II-DNA/RNA
+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: template DNA
+Macromolecule #14: nontemplate DNA
+Macromolecule #15: 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 |
Grid | Details: Lacey carbon copper grids (Quantifoil) |
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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 37169 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 2972 / Average electron dose: 25 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.6 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 240 A2 was applied. Number images used: 14777 |
Details | Particles were picked using EMAN2 and were processed using RELION 1.2. |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: E / Chain - #4 - Chain ID: F / Chain - #5 - Chain ID: H / Chain - #6 - Chain ID: I / Chain - #7 - Chain ID: J / Chain - #8 - Chain ID: K / Chain - #9 - Chain ID: L |
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Software | Name: SITUS |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4v1m: |