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Yorodumi- EMDB-40968: Atomic model of the mammalian Mediator complex with MED26 subunit -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40968 | |||||||||
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Title | Atomic model of the mammalian Mediator complex with MED26 subunit | |||||||||
Map data | Atomic model of the mammalian Mediator complex with MED26 subunit | |||||||||
Sample |
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Keywords | mouse mediator / complex / GENE REGULATION / MED26 subunit | |||||||||
Function / homology | Function and homology information positive regulation of T cell extravasation / Nuclear Receptor transcription pathway / 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 / retinal pigment epithelium development / mammary gland branching involved in thelarche ...positive regulation of T cell extravasation / Nuclear Receptor transcription pathway / 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 / retinal pigment epithelium development / mammary gland branching involved in thelarche / G0 to G1 transition / thyroid hormone receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / core mediator complex / regulation of vitamin D receptor signaling pathway / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / nuclear retinoic acid receptor binding / mediator complex / positive regulation of keratinocyte differentiation / embryonic heart tube development / camera-type eye development / cellular response to thyroid hormone stimulus / positive regulation of hepatocyte proliferation / embryonic hindlimb morphogenesis / nuclear vitamin D receptor binding / peroxisome proliferator activated receptor binding / limb development / lens development in camera-type eye / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / nuclear thyroid hormone receptor binding / mammary gland epithelial cell proliferation / megakaryocyte development / histone acetyltransferase binding / cellular response to hepatocyte growth factor stimulus / cortical actin cytoskeleton / termination of RNA polymerase II transcription / LBD domain binding / epithelial cell proliferation involved in mammary gland duct elongation / fat cell differentiation / skeletal muscle cell differentiation / mammary gland branching involved in pregnancy / somatic stem cell population maintenance / monocyte differentiation / blastocyst development / general transcription initiation factor binding / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of fibroblast proliferation / ubiquitin ligase complex / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / cellular response to epidermal growth factor stimulus / peroxisome proliferator activated receptor signaling pathway / lactation / positive regulation of erythrocyte differentiation / nuclear receptor coactivator activity / liver development / promoter-specific chromatin binding / nuclear estrogen receptor binding / nuclear receptor binding / protein-DNA complex / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / animal organ morphogenesis / mRNA transcription by RNA polymerase II / cell morphogenesis / brain development / chromatin DNA binding / transcription coactivator binding / protein import into nucleus / transcription corepressor activity / ubiquitin protein ligase activity / actin binding / heart development / angiogenesis / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor 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 / chromatin binding / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of gene expression Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.68 Å | |||||||||
Authors | Zhao H / Asturias F | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Mol Cell / Year: 2024 Title: An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II. Authors: Haiyan Zhao / Jiaqin Li / Yufei Xiang / Sohail Malik / Supriya V Vartak / Giovana M B Veronezi / Natalie Young / McKayla Riney / Jens Kalchschmidt / Andrea Conte / Seol Kyoung Jung / ...Authors: Haiyan Zhao / Jiaqin Li / Yufei Xiang / Sohail Malik / Supriya V Vartak / Giovana M B Veronezi / Natalie Young / McKayla Riney / Jens Kalchschmidt / Andrea Conte / Seol Kyoung Jung / Srinivas Ramachandran / Robert G Roeder / Yi Shi / Rafael Casellas / Francisco J Asturias / Abstract: The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent ...The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent transcription remains unknown. We investigated modulation of metazoan MED interaction with RNA polymerase II (RNA Pol II) by antagonistic effects of the MED26 subunit and the CDK8 kinase module (CKM). Biochemical analysis of CKM-MED showed that the CKM blocks binding of the RNA Pol II carboxy-terminal domain (CTD), preventing RNA Pol II interaction. This restriction is eliminated by nuclear receptor (NR) binding to CKM-MED, which enables CTD binding in a MED26-dependent manner. Cryoelectron microscopy (cryo-EM) and crosslinking-mass spectrometry (XL-MS) revealed that the structural basis for modulation of CTD interaction with MED relates to a large intrinsically disordered region (IDR) in CKM subunit MED13 that blocks MED26 and CTD interaction with MED but is repositioned upon NR binding. Hence, NRs can control transcription initiation by priming CKM-MED for MED26-dependent RNA Pol II interaction. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40968.map.gz | 333.5 MB | EMDB map data format | |
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Header (meta data) | emd-40968-v30.xml emd-40968.xml | 49 KB 49 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40968_fsc.xml | 25.8 KB | Display | FSC data file |
Images | emd_40968.png | 83.2 KB | ||
Filedesc metadata | emd-40968.cif.gz | 14.2 KB | ||
Others | emd_40968_half_map_1.map.gz emd_40968_half_map_2.map.gz | 622.5 MB 622.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40968 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40968 | HTTPS FTP |
-Validation report
Summary document | emd_40968_validation.pdf.gz | 965.1 KB | Display | EMDB validaton report |
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Full document | emd_40968_full_validation.pdf.gz | 964.7 KB | Display | |
Data in XML | emd_40968_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | emd_40968_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40968 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40968 | HTTPS FTP |
-Related structure data
Related structure data | 8t1iMC 8t9dC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40968.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Atomic model of the mammalian Mediator complex with MED26 subunit | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_40968_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_40968_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
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 26
+Macromolecule #22: Mediator of RNA polymerase II transcription subunit 27
+Macromolecule #23: Mediator of RNA polymerase II transcription subunit 28
+Macromolecule #24: Mediator of RNA polymerase II transcription subunit 29
+Macromolecule #25: Mediator of RNA polymerase II transcription subunit 30
+Macromolecule #26: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #27: Unknown Peptide
-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 |
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 / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |