+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8480 | |||||||||
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Title | Cryo-EM map of the Mediator-RNAPII complex | |||||||||
Map data | Mediator-RNAPII complex | |||||||||
Sample |
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Function / homology | Function and homology information RNA Polymerase II Transcription Elongation / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / 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 Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter ...RNA Polymerase II Transcription Elongation / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / 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 Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA polymerase II, holoenzyme / Formation of the Early Elongation Complex / RNA Polymerase I Promoter Escape / Formation of TC-NER Pre-Incision Complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / : / termination of RNA polymerase II transcription, poly(A)-coupled / regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / DNA-templated transcription elongation / : / core mediator complex / mediator complex / termination of RNA polymerase II transcription / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase I / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription by RNA polymerase III / RNA polymerase II activity / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / pericentric heterochromatin / transcription coregulator activity / translation initiation factor binding / transcription initiation at RNA polymerase II promoter / P-body / euchromatin / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein-macromolecule adaptor activity / single-stranded DNA binding / transcription coactivator activity / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleotide binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / DNA binding / RNA binding / zinc ion binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) / Fission yeast (fission yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.8 Å | |||||||||
Authors | Tsai K-L / Yu X / Gopalan S / Chao T-C / Zhang Y / Florens L / Washburn MP / Murakami K / Conaway RC / Conaway JW / Asturias F | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nature / Year: 2017 Title: Mediator structure and rearrangements required for holoenzyme formation. Authors: Kuang-Lei Tsai / Xiaodi Yu / Sneha Gopalan / Ti-Chun Chao / Ying Zhang / Laurence Florens / Michael P Washburn / Kenji Murakami / Ronald C Conaway / Joan W Conaway / Francisco J Asturias / Abstract: The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is ...The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals. | |||||||||
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_8480.map.gz | 19.4 MB | EMDB map data format | |
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Header (meta data) | emd-8480-v30.xml emd-8480.xml | 43.3 KB 43.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8480_fsc_1.xml emd_8480_fsc_2.xml | 6.3 KB 6.3 KB | Display Display | FSC data file |
Images | emd_8480.png | 275.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8480 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8480 | HTTPS FTP |
-Validation report
Summary document | emd_8480_validation.pdf.gz | 476.8 KB | Display | EMDB validaton report |
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Full document | emd_8480_full_validation.pdf.gz | 476.3 KB | Display | |
Data in XML | emd_8480_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | emd_8480_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8480 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8480 | HTTPS FTP |
-Related structure data
Related structure data | 5u0sMC 8479C 5u0pC C: citing same article (ref.) M: atomic model generated by this map |
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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_8480.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mediator-RNAPII complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.62 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 : complex of Mediator and RNAPII
+Supramolecule #1: complex of Mediator and RNAPII
+Macromolecule #1: Mediator complex subunit 6
+Macromolecule #2: Mediator complex subunit 8
+Macromolecule #3: Mediator complex subunit 17
+Macromolecule #4: Mediator complex subunit 18
+Macromolecule #5: Mediator complex subunit 20
+Macromolecule #6: Mediator complex subunit 11
+Macromolecule #7: Mediator complex subunit 22
+Macromolecule #8: Mediator complex subunit 14
+Macromolecule #9: Mediator complex subunit 4
+Macromolecule #10: Mediator complex subunit 7
+Macromolecule #11: Mediator complex subunit 21
+Macromolecule #12: Mediator complex subunit 31
+Macromolecule #13: Mediator complex subunit 27
+Macromolecule #14: Mediator complex subunit 9
+Macromolecule #15: Mediator complex subunit 19
+Macromolecule #16: Mediator complex subunit 10
+Macromolecule #17: RNA polymerase II subunit Rpb1
+Macromolecule #18: RNA polymerase II subunit Rpb2
+Macromolecule #19: RNA polymerase II subunit Rpb3
+Macromolecule #20: RNA polymerase II subunit Rpb4
+Macromolecule #21: RNA polymerase II subunit Rpb5
+Macromolecule #22: RNA polymerase II subunit Rpb6
+Macromolecule #23: RNA polymerase II subunit Rpb7
+Macromolecule #24: RNA polymerase II subunit Rpb8
+Macromolecule #25: RNA polymerase II subunit Rpb9
+Macromolecule #26: RNA polymerase II subunit Rpb10
+Macromolecule #27: RNA polymerase II subunit Rpb11
+Macromolecule #28: RNA polymerase II subunit Rpb12
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 Details: 20 mM HEPES, pH 7.4, 200 mM potassium acetate, 5 mM b-Mercaptoethanol, 0.01% NP-40 |
Grid | Model: C-flat-2/2 4C / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 7.0 sec. / Average electron dose: 9.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |