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Yorodumi- EMDB-7334: Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7334 | ||||||||||||
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Title | Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Compact Active State | ||||||||||||
Map data | primary map | ||||||||||||
Sample |
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Function / homology | Function and homology information protein localization to pericentric heterochromatin / regulation of kidney development / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of striated muscle cell differentiation / sex chromatin / CAF-1 complex / negative regulation of keratinocyte differentiation ...protein localization to pericentric heterochromatin / regulation of kidney development / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of striated muscle cell differentiation / sex chromatin / CAF-1 complex / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / random inactivation of X chromosome / primary miRNA binding / ubiquitin-modified histone reader activity / regulatory ncRNA-mediated heterochromatin formation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / response to tetrachloromethane / cerebellar cortex development / facultative heterochromatin formation / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / positive regulation of cell cycle G1/S phase transition / negative regulation of cardiac muscle cell proliferation / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / chromatin silencing complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / protein-lysine N-methyltransferase activity / negative regulation of stem cell differentiation / RSC-type complex / Transcription of E2F targets under negative control by DREAM complex / pronucleus / cardiac muscle hypertrophy in response to stress / Polo-like kinase mediated events / synaptic transmission, GABAergic / G0 and Early G1 / positive regulation of dendrite development / histone H3 methyltransferase activity / lncRNA binding / cardiac muscle cell proliferation / Cyclin E associated events during G1/S transition / SUMOylation of chromatin organization proteins / histone methyltransferase complex / negative regulation of G1/S transition of mitotic cell cycle / G1 to G0 transition / negative regulation of gene expression, epigenetic / spinal cord development / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / ATPase complex / histone methyltransferase activity / Sin3-type complex / Cyclin A:Cdk2-associated events at S phase entry / oligodendrocyte differentiation / negative regulation of transcription elongation by RNA polymerase II / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / negative regulation of cell differentiation / histone deacetylase complex / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / subtelomeric heterochromatin formation / negative regulation of cytokine production involved in inflammatory response / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / ribonucleoprotein complex binding / positive regulation of epithelial to mesenchymal transition / Deposition of new CENPA-containing nucleosomes at the centromere / keratinocyte differentiation / transcription coregulator activity / spleen development / protein localization to chromatin / enzyme activator activity / Regulation of TP53 Activity through Acetylation / Regulation of PTEN gene transcription / methylated histone binding / liver regeneration / B cell differentiation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription corepressor binding / PRC2 methylates histones and DNA / positive regulation of MAP kinase activity / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of GTPase activity / thymus development / liver development / negative regulation of cell migration / Defective pyroptosis / ubiquitin binding / HDACs deacetylate histones / cellular response to leukemia inhibitory factor / central nervous system development / stem cell differentiation / regulation of circadian rhythm / promoter-specific chromatin binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Kasinath V / Faini M / Poepsel S / Reif D / Feng A / Stjepanovic G / Aebersold R / Nogales E | ||||||||||||
Funding support | United States, European Union, 3 items
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Citation | Journal: Science / Year: 2018 Title: Structures of human PRC2 with its cofactors AEBP2 and JARID2. Authors: Vignesh Kasinath / Marco Faini / Simon Poepsel / Dvir Reif / Xinyu Ashlee Feng / Goran Stjepanovic / Ruedi Aebersold / Eva Nogales / Abstract: Transcriptionally repressive histone H3 lysine 27 methylation by Polycomb repressive complex 2 (PRC2) is essential for cellular differentiation and development. Here we report cryo-electron ...Transcriptionally repressive histone H3 lysine 27 methylation by Polycomb repressive complex 2 (PRC2) is essential for cellular differentiation and development. Here we report cryo-electron microscopy structures of human PRC2 in a basal state and two distinct active states while in complex with its cofactors JARID2 and AEBP2. Both cofactors mimic the binding of histone H3 tails. JARID2, methylated by PRC2, mimics a methylated H3 tail to stimulate PRC2 activity, whereas AEBP2 interacts with the RBAP48 subunit, mimicking an unmodified H3 tail. SUZ12 interacts with all other subunits within the assembly and thus contributes to the stability of the complex. Our analysis defines the complete architecture of a functionally relevant PRC2 and provides a structural framework to understand its regulation by cofactors, histone tails, and RNA. | ||||||||||||
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_7334.map.gz | 85.2 MB | EMDB map data format | |
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Header (meta data) | emd-7334-v30.xml emd-7334.xml | 25.8 KB 25.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7334_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_7334.png | 49.7 KB | ||
Others | emd_7334_half_map_1.map.gz emd_7334_half_map_2.map.gz | 71.4 MB 71.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7334 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7334 | HTTPS FTP |
-Validation report
Summary document | emd_7334_validation.pdf.gz | 821.7 KB | Display | EMDB validaton report |
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Full document | emd_7334_full_validation.pdf.gz | 821.3 KB | Display | |
Data in XML | emd_7334_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | emd_7334_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7334 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7334 | HTTPS FTP |
-Related structure data
Related structure data | 6c23MC 7335C 7337C 6c24C M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_7334.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map p1
File | emd_7334_half_map_1.map | ||||||||||||
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Annotation | Half map p1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map p2
File | emd_7334_half_map_2.map | ||||||||||||
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Annotation | Half map p2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Ternary complex of PRC2 with cofactors AEBP2 and JARID2
+Supramolecule #1: Ternary complex of PRC2 with cofactors AEBP2 and JARID2
+Macromolecule #1: Polycomb protein SUZ12
+Macromolecule #2: Protein Jumonji
+Macromolecule #3: Histone-lysine N-methyltransferase EZH2
+Macromolecule #4: Polycomb protein EED
+Macromolecule #5: Histone-binding protein RBBP4
+Macromolecule #6: JARID2-substrate
+Macromolecule #7: Zinc finger protein AEBP2
+Macromolecule #8: SUZ12
+Macromolecule #9: Protein Jumonji
-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 TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |