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Yorodumi- PDB-7enj: Human Mediator (deletion of MED1-IDR) in a Tail-bent conformation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7enj | ||||||
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Title | Human Mediator (deletion of MED1-IDR) in a Tail-bent conformation (MED-B) | ||||||
Components |
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Keywords | TRANSCRIPTION / Mediator complex | ||||||
Function / homology | Function and homology information positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / mammary gland branching involved in thelarche / retinal pigment epithelium development / G0 to G1 transition ...positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / mammary gland branching involved in thelarche / retinal pigment epithelium development / G0 to G1 transition / thyroid hormone receptor signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / mediator complex / nuclear retinoic acid receptor binding / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of hepatocyte proliferation / nuclear vitamin D receptor binding / limb development / lens development in camera-type eye / nuclear thyroid hormone receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / megakaryocyte development / cellular response to steroid hormone stimulus / cellular response to hepatocyte growth factor stimulus / histone acetyltransferase binding / termination of RNA polymerase II transcription / cortical actin cytoskeleton / RSV-host interactions / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / fat cell differentiation / skeletal muscle cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / somatic stem cell population maintenance / blastocyst development / general transcription initiation factor binding / negative regulation of keratinocyte proliferation / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / negative regulation of fibroblast proliferation / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / cellular response to epidermal growth factor stimulus / lactation / Regulation of lipid metabolism by PPARalpha / positive regulation of erythrocyte differentiation / liver development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / nuclear receptor binding / nuclear estrogen receptor binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / Heme signaling / brain development / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / DNA-directed 5'-3' RNA polymerase activity / protein import into nucleus / transcription corepressor activity / ubiquitin protein ligase activity / Circadian Clock / actin binding / angiogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / nuclear body / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
Authors | Yin, X. / Li, J. / Wu, Z. / Liu, W. / Xu, Y. | ||||||
Citation | Journal: Science / Year: 2021 Title: Structures of the human Mediator and Mediator-bound preinitiation complex. Authors: Xizi Chen / Xiaotong Yin / Jiabei Li / Zihan Wu / Yilun Qi / Xinxin Wang / Weida Liu / Yanhui Xu / Abstract: The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26- ...The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of the Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module-extended (at near-atomic resolution) and Tail-bent conformations and structures of TFIID-based PIC-Mediator (76 polypeptides, ~4.1 megadaltons) in four distinct conformations. PIC-Mediator assembly induces concerted reorganization (Head-tilting and Middle-down) of Mediator and creates a Head-Middle sandwich, which stabilizes two CTD segments and brings CTD to CDK7 for phosphorylation; this suggests a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the importance of TFIID in orchestrating PIC-Mediator assembly. | ||||||
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 | 7enj.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7enj.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 7enj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7enj_validation.pdf.gz | 921.7 KB | Display | wwPDB validaton report |
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Full document | 7enj_full_validation.pdf.gz | 1005 KB | Display | |
Data in XML | 7enj_validation.xml.gz | 167.6 KB | Display | |
Data in CIF | 7enj_validation.cif.gz | 273.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/7enj ftp://data.pdbj.org/pub/pdb/validation_reports/en/7enj | HTTPS FTP |
-Related structure data
Related structure data | 31211MC 7emfC 7enaC 7encC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Mediator of RNA polymerase II transcription subunit ... , 24 types, 24 molecules ADFGIJKNOPQRSTUVWXZ01234
-Protein/peptide / Protein / Non-polymers , 3 types, 3 molecules BH
#27: Chemical | ChemComp-ZN / |
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#2: Protein/peptide | Mass: 1720.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#6: Protein | Mass: 29112.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MED8 / Production host: Homo sapiens (human) / References: UniProt: Q96G25 |
-Details
Has ligand of interest | N |
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-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: Structure of the human Mediator complex / Type: COMPLEX / Entity ID: #1-#26 / Source: RECOMBINANT |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: Expi293 |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 32 |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62871 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |