+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21514 | |||||||||
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Title | map of the mammalian Mediator complex | |||||||||
Map data | Mammalian Mediator complex | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / core mediator complex / nuclear retinoic acid receptor binding / mediator complex / limb development / nuclear thyroid hormone receptor binding / cortical actin cytoskeleton / termination of RNA polymerase II transcription / skeletal muscle cell differentiation ...positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / core mediator complex / nuclear retinoic acid receptor binding / mediator complex / limb development / nuclear thyroid hormone receptor binding / cortical actin cytoskeleton / termination of RNA polymerase II transcription / skeletal muscle cell differentiation / somatic stem cell population maintenance / blastocyst development / positive regulation of transcription initiation by RNA polymerase II / nuclear retinoid X receptor binding / negative regulation of fibroblast proliferation / ubiquitin ligase complex / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / nuclear receptor coactivator activity / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / transcription coactivator binding / ubiquitin protein ligase activity / actin binding / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / cytoskeleton / nuclear body / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein-containing complex binding / positive regulation of gene expression / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Mouse (mice) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.02 Å | |||||||||
Authors | Zhao H / Young N / Asturias F | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Cell / Year: 2019 Title: A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers. Authors: Laila El Khattabi / Haiyan Zhao / Jens Kalchschmidt / Natalie Young / Seolkyoung Jung / Peter Van Blerkom / Philippe Kieffer-Kwon / Kyong-Rim Kieffer-Kwon / Solji Park / Xiang Wang / Jordan ...Authors: Laila El Khattabi / Haiyan Zhao / Jens Kalchschmidt / Natalie Young / Seolkyoung Jung / Peter Van Blerkom / Philippe Kieffer-Kwon / Kyong-Rim Kieffer-Kwon / Solji Park / Xiang Wang / Jordan Krebs / Subhash Tripathi / Noboru Sakabe / Débora R Sobreira / Su-Chen Huang / Suhas S P Rao / Nathanael Pruett / Daniel Chauss / Erica Sadler / Andrea Lopez / Marcelo A Nóbrega / Erez Lieberman Aiden / Francisco J Asturias / Rafael Casellas / Abstract: While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron ...While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure of mammalian Mediator (mMED). Deletion analyses in B, T, and embryonic stem cells (ESC) identified a core of essential subunits required for Pol II recruitment genome-wide. Conversely, loss of non-essential subunits mostly affects promoters linked to multiple enhancers. Contrary to current models, however, mMED and Pol II are dispensable to physically tether regulatory DNA, a topological activity requiring architectural proteins. Cryo-EM analysis revealed a conserved core, with non-essential subunits increasing structural complexity of the tail module, a primary transcription factor target. Changes in tail structure markedly increase Pol II and kinase module interactions. We propose that Mediator's structural pliability enables it to integrate and transmit regulatory signals and act as a functional, rather than an architectural bridge, between promoters and enhancers. | |||||||||
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_21514.map.gz | 621.2 MB | EMDB map data format | |
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Header (meta data) | emd-21514-v30.xml emd-21514.xml | 44.9 KB 44.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21514_fsc.xml | 21.2 KB | Display | FSC data file |
Images | emd_21514.png | 133.7 KB | ||
Others | emd_21514_additional_1.map.gz emd_21514_additional_2.map.gz | 527.6 MB 10.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21514 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21514 | HTTPS FTP |
-Validation report
Summary document | emd_21514_validation.pdf.gz | 585.6 KB | Display | EMDB validaton report |
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Full document | emd_21514_full_validation.pdf.gz | 585.2 KB | Display | |
Data in XML | emd_21514_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | emd_21514_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21514 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21514 | HTTPS FTP |
-Related structure data
Related structure data | 6w1sMC 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_21514.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mammalian Mediator complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Mammalian Mediator complex
File | emd_21514_additional_1.map | ||||||||||||
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Annotation | Mammalian Mediator complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Mammalian Mediator complex
File | emd_21514_additional_2.map | ||||||||||||
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Annotation | Mammalian Mediator complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mouse mediator complex
+Supramolecule #1: Mouse mediator complex
+Macromolecule #1: Mediator of RNA polymerase II transcription subunit 1
+Macromolecule #2: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #3: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #4: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #5: Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #6: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #7: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #8: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #9: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #10: Mediator of RNA polymerase II transcription subunit 15
+Macromolecule #11: Mediator of RNA polymerase II transcription subunit 16
+Macromolecule #12: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #13: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #14: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #15: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #16: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #17: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #18: Mediator of RNA polymerase II transcription subunit 23
+Macromolecule #19: Mediator of RNA polymerase II transcription subunit 24
+Macromolecule #20: Mediator of RNA polymerase II transcription subunit 25
+Macromolecule #21: Mediator of RNA polymerase II transcription subunit 27
+Macromolecule #22: Mediator of RNA polymerase II transcription subunit 28
+Macromolecule #23: Mediator of RNA polymerase II transcription subunit 29
+Macromolecule #24: Mediator of RNA polymerase II transcription subunit 30
+Macromolecule #25: Mediator of RNA polymerase II transcription subunit 31
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.9 |
Sugar embedding | Material: ice |
Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 30.0 nm / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 22.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |