+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41107 | |||||||||
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Title | CryoEM structure of TR-TRAP | |||||||||
Map data | Structure of TR-TRAP | |||||||||
Sample |
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Keywords | TR-TRAP / mediator / CKM module / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of mediator complex assembly / positive regulation of T cell extravasation / CKM complex / 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 ...positive regulation of mediator complex assembly / positive regulation of T cell extravasation / CKM complex / 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 / triglyceride homeostasis / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of hepatocyte proliferation / positive regulation of chromatin binding / 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 / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / RSV-host interactions / 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 neuron differentiation / hematopoietic stem cell differentiation / negative regulation of keratinocyte proliferation / embryonic placenta development / 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 / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / lactation / cellular response to epidermal growth factor stimulus / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of erythrocyte differentiation / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / liver development / cholesterol homeostasis / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / brain development / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.66 Å | |||||||||
Authors | Zhao H / Asturias F | |||||||||
Funding support | United States, 1 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_41107.map.gz | 590.7 MB | EMDB map data format | |
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Header (meta data) | emd-41107-v30.xml emd-41107.xml | 48.6 KB 48.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41107_fsc.xml | 25.8 KB | Display | FSC data file |
Images | emd_41107.png | 68.9 KB | ||
Filedesc metadata | emd-41107.cif.gz | 14.8 KB | ||
Others | emd_41107_half_map_1.map.gz emd_41107_half_map_2.map.gz | 579.6 MB 579.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41107 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41107 | HTTPS FTP |
-Validation report
Summary document | emd_41107_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_41107_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_41107_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | emd_41107_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41107 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41107 | HTTPS FTP |
-Related structure data
Related structure data | 8t9dMC 8t1iC 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_41107.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Structure of TR-TRAP | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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 2
File | emd_41107_half_map_1.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_41107_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : mediator complex with transcription factor TR
+Supramolecule #1: mediator complex with transcription factor TR
+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 20
+Macromolecule #15: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #16: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #17: Mediator of RNA polymerase II transcription subunit 23
+Macromolecule #18: Mediator of RNA polymerase II transcription subunit 24
+Macromolecule #19: Mediator of RNA polymerase II transcription subunit 25
+Macromolecule #20: Mediator of RNA polymerase II transcription subunit 27
+Macromolecule #21: Mediator of RNA polymerase II transcription subunit 28
+Macromolecule #22: Mediator of RNA polymerase II transcription subunit 29
+Macromolecule #23: Mediator of RNA polymerase II transcription subunit 30
+Macromolecule #24: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #25: Unknown Peptide
+Macromolecule #26: Mediator of RNA polymerase II transcription subunit 13
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 35.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |