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Yorodumi- EMDB-8831: Structural and functional impacts of ER coactivator sequential re... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8831 | |||||||||
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Title | Structural and functional impacts of ER coactivator sequential recruitment | |||||||||
Map data | ERa/SRC-3a/p300 complex without SRC-3b and CARM1 | |||||||||
Sample |
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Function / homology | Function and homology information : / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal ...: / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / positive regulation of epithelial cell apoptotic process / positive regulation of transcription by RNA polymerase I / histone methyltransferase activity / nuclear replication fork / positive regulation of fat cell differentiation / response to cAMP / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / BMAL1:CLOCK,NPAS2 activates circadian gene expression / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / lysine-acetylated histone binding / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / RMTs methylate histone arginines / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Circadian Clock / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 22.0 Å | |||||||||
Authors | Yi P / Wang Z / Feng Q / Chou CK / Pintilie G / Shen H / Foulds CE / Fan GZ / Serysheva I / Ludtke S ...Yi P / Wang Z / Feng Q / Chou CK / Pintilie G / Shen H / Foulds CE / Fan GZ / Serysheva I / Ludtke S / Schmid MF / Hung MC / Chiu W / OMalley BW | |||||||||
Citation | Journal: Mol Cell / Year: 2017 Title: Structural and Functional Impacts of ER Coactivator Sequential Recruitment. Authors: Ping Yi / Zhao Wang / Qin Feng / Chao-Kai Chou / Grigore D Pintilie / Hong Shen / Charles E Foulds / Guizhen Fan / Irina Serysheva / Steven J Ludtke / Michael F Schmid / Mien-Chie Hung / Wah ...Authors: Ping Yi / Zhao Wang / Qin Feng / Chao-Kai Chou / Grigore D Pintilie / Hong Shen / Charles E Foulds / Guizhen Fan / Irina Serysheva / Steven J Ludtke / Michael F Schmid / Mien-Chie Hung / Wah Chiu / Bert W O'Malley / Abstract: Nuclear receptors recruit multiple coactivators sequentially to activate transcription. This "ordered" recruitment allows different coactivator activities to engage the nuclear receptor complex at ...Nuclear receptors recruit multiple coactivators sequentially to activate transcription. This "ordered" recruitment allows different coactivator activities to engage the nuclear receptor complex at different steps of transcription. Estrogen receptor (ER) recruits steroid receptor coactivator-3 (SRC-3) primary coactivator and secondary coactivators, p300/CBP and CARM1. CARM1 recruitment lags behind the binding of SRC-3 and p300 to ER. Combining cryo-electron microscopy (cryo-EM) structure analysis and biochemical approaches, we demonstrate that there is a close crosstalk between early- and late-recruited coactivators. The sequential recruitment of CARM1 not only adds a protein arginine methyltransferase activity to the ER-coactivator complex, it also alters the structural organization of the pre-existing ERE/ERα/SRC-3/p300 complex. It induces a p300 conformational change and significantly increases p300 HAT activity on histone H3K18 residues, which, in turn, promotes CARM1 methylation activity on H3R17 residues to enhance transcriptional activity. This study reveals a structural role for a coactivator sequential recruitment and biochemical process in ER-mediated transcription. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8831.map.gz | 7.1 MB | EMDB map data format | |
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Header (meta data) | emd-8831-v30.xml emd-8831.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_8831.png | 254.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8831 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8831 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8831.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ERa/SRC-3a/p300 complex without SRC-3b and CARM1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ER coactivators complex
Entire | Name: ER coactivators complex |
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Components |
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-Supramolecule #1: ER coactivators complex
Supramolecule | Name: ER coactivators complex / type: complex / ID: 1 / Parent: 0 / Details: map of ER complex with CARM1 bind |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Baculoviridae (virus) / Recombinant cell: sf9 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - Film thickness: 30.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 23000 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 2-40 / Number grids imaged: 5 / Average exposure time: 8.0 sec. / Average electron dose: 20.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: e2ctf.py / Software - details: use e2ctf auto correct ctf |
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Startup model | Type of model: OTHER / Details: generate from scratch in EMAN2 |
Initial angle assignment | Type: PROJECTION MATCHING Projection matching processing - Number reference projections: 1096 Projection matching processing - Merit function: CC Projection matching processing - Angular sampling: 2.0 degrees Software - Name: EMAN2 |
Final 3D classification | Number classes: 3 / Avg.num./class: 5000 / Software - Name: EMAN2 / Details: use eman2 multi refine to separate classes in 3D |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: EMAN2 |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Details: done by EMAN2 automatically / Number images used: 46527 |
Details | running in super resolution counting mode through serialEM |