+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8479 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM map of the transcriptional Mediator | |||||||||
Map data | Sp Mediator | |||||||||
Sample |
| |||||||||
Keywords | transcription / transcriptional / Mediator / Head / Middle / Tail / Srb / RNA polymerase II / Med | |||||||||
Function / homology | Function and homology information core mediator complex / mediator complex / termination of RNA polymerase II transcription / positive regulation of transcription initiation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / euchromatin / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II ...core mediator complex / mediator complex / termination of RNA polymerase II transcription / positive regulation of transcription initiation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / euchromatin / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Tsai K-L / Yu X | |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8479.map.gz | 154.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-8479-v30.xml emd-8479.xml | 29.5 KB 29.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8479_fsc.xml | 12.3 KB | Display | FSC data file |
Images | emd_8479.png | 22.1 KB | ||
Masks | emd_8479_msk_1.map | 166.4 MB | Mask map | |
Filedesc metadata | emd-8479.cif.gz | 7.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8479 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8479 | HTTPS FTP |
-Related structure data
Related structure data | 5u0pMC 8480C 5u0sC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_8479.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sp Mediator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_8479_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Mediator complex
+Supramolecule #1: Mediator complex
+Macromolecule #1: Mediator complex subunit 14
+Macromolecule #2: Mediator complex subunit 6
+Macromolecule #3: Mediator complex subunit 8
+Macromolecule #4: Mediator complex subunit 17
+Macromolecule #5: Mediator complex subunit 18
+Macromolecule #6: Mediator complex subunit 20
+Macromolecule #7: Mediator complex subunit 11
+Macromolecule #8: Mediator complex subunit 22
+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 9
+Macromolecule #14: Mediator complex subunit 27
+Macromolecule #15: Mediator complex subunit 19
+Macromolecule #16: Mediator complex subunit 10
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
---|---|
Buffer | pH: 7.4 Details: 20 mM HEPES, pH 7.4, 200 mM potassium acetate, 5 mM b-Mercaptoethanol, 0.01% NP-40 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 FIELDBright-field microscopy / 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 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 11181 / Average exposure time: 7.0 sec. / Average electron dose: 9.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |