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Open data
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Basic information
Entry | Database: PDB / ID: 8trh | ||||||
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Title | The IDRc bound human core Mediator complex | ||||||
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![]() | TRANSCRIPTION / Mediator. | ||||||
Function / homology | ![]() positive regulation of T cell extravasation / CKM complex / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition ...positive regulation of T cell extravasation / CKM complex / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / G0 to G1 transition / mammary gland branching involved in thelarche / thyroid hormone receptor signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / mediator complex / positive regulation of keratinocyte differentiation / thyroid hormone generation / Generic Transcription Pathway / peroxisome proliferator activated receptor binding / embryonic heart tube development / cellular response to thyroid hormone stimulus / positive regulation of hepatocyte proliferation / nuclear vitamin D receptor binding / embryonic hindlimb morphogenesis / nuclear thyroid hormone receptor binding / lens development in camera-type eye / limb development / embryonic hemopoiesis / triglyceride homeostasis / megakaryocyte development / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / cortical actin cytoskeleton / positive regulation of intracellular estrogen receptor signaling pathway / histone acetyltransferase binding / LBD domain binding / epithelial cell proliferation involved in mammary gland duct elongation / RSV-host interactions / erythrocyte development / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / skeletal muscle cell differentiation / general transcription initiation factor binding / blastocyst development / somatic stem cell population maintenance / animal organ regeneration / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / ubiquitin ligase complex / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / nuclear receptor-mediated steroid hormone signaling pathway / RNA polymerase II preinitiation complex assembly / negative regulation of fibroblast proliferation / keratinocyte differentiation / lactation / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / cellular response to epidermal growth factor stimulus / positive regulation of erythrocyte differentiation / cholesterol homeostasis / nuclear estrogen receptor binding / nuclear receptor binding / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / chromatin DNA binding / mRNA transcription by RNA polymerase II / promoter-specific chromatin binding / liver development / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / protein-DNA complex / Cytoprotection by HMOX1 / cell morphogenesis / brain development / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / transcription coactivator binding / : / protein import into nucleus / DNA-directed RNA polymerase activity / transcription corepressor activity / ubiquitin protein ligase activity / actin binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / angiogenesis / transcription regulator complex / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / transcription coactivator activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
![]() | Chen, S.F. / Chao, T.C. / Kim, H.J. / Tang, H.C. / Khadka, S. / Li, T. / Murakami, K. / Boyer, T.G. / Tsai, K.L. | ||||||
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![]() | ![]() Title: Structural basis of the human transcriptional Mediator regulated by its dissociable kinase module. Authors: Ti-Chun Chao / Shin-Fu Chen / Hee Jong Kim / Hui-Chi Tang / Hsiang-Ching Tseng / An Xu / Leon Palao / Subash Khadka / Tao Li / Mo-Fan Huang / Dung-Fang Lee / Kenji Murakami / Thomas G Boyer / Kuang-Lei Tsai / ![]() Abstract: The eukaryotic transcriptional Mediator comprises a large core (cMED) and a dissociable CDK8 kinase module (CKM). cMED recruits RNA polymerase II (RNA Pol II) and promotes pre-initiation complex ...The eukaryotic transcriptional Mediator comprises a large core (cMED) and a dissociable CDK8 kinase module (CKM). cMED recruits RNA polymerase II (RNA Pol II) and promotes pre-initiation complex formation in a manner repressed by the CKM through mechanisms presently unknown. Herein, we report cryoelectron microscopy structures of the complete human Mediator and its CKM. The CKM binds to multiple regions on cMED through both MED12 and MED13, including a large intrinsically disordered region (IDR) in the latter. MED12 and MED13 together anchor the CKM to the cMED hook, positioning CDK8 downstream and proximal to the transcription start site. Notably, the MED13 IDR obstructs the recruitment of RNA Pol II/MED26 onto cMED by direct occlusion of their respective binding sites, leading to functional repression of cMED-dependent transcription. Combined with biochemical and functional analyses, these structures provide a conserved mechanistic framework to explain the basis for CKM-mediated repression of cMED function. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 203.1 KB | Display | |
Data in CIF | ![]() | 309.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 41580MC ![]() 8tq2C ![]() 8tqcC ![]() 8tqwC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
+Mediator of RNA polymerase II transcription subunit ... , 25 types, 25 molecules 01234ADFGHIJKNOPQRTVWXdSU
-Protein/peptide / Non-polymers , 2 types, 3 molecules B

#27: Chemical | #7: Protein/peptide | | Mass: 1720.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: The IDRc bound human core Mediator complex / Type: COMPLEX / Entity ID: #1-#26 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97904 / Symmetry type: POINT |