+Open data
-Basic information
Entry | Database: PDB / ID: 6w1s | |||||||||
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Title | Atomic model of the mammalian Mediator complex | |||||||||
Components | (Mediator of RNA polymerase II transcription subunit ...) x 25 | |||||||||
Keywords | GENE REGULATION / mouse mediator / complex | |||||||||
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) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.02 Å | |||||||||
Authors | Zhao, H. / Young, N. / Asturias, F. | |||||||||
Funding support | United States, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6w1s.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6w1s.ent.gz | 900.5 KB | Display | PDB format |
PDBx/mmJSON format | 6w1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w1s_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6w1s_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6w1s_validation.xml.gz | 169.4 KB | Display | |
Data in CIF | 6w1s_validation.cif.gz | 276.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/6w1s ftp://data.pdbj.org/pub/pdb/validation_reports/w1/6w1s | HTTPS FTP |
-Related structure data
Related structure data | 21514MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
+Mediator of RNA polymerase II transcription subunit ... , 25 types, 25 molecules ABCDEFGHIJKLMNOPQRSTVWXYZ
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mouse mediator complex / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 1.0 MDa / Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) |
Buffer solution | pH: 7.9 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon |
EM embedding | Material: ice |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 22.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 217557 / Symmetry type: POINT |