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Yorodumi- EMDB-7335: Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7335 | ||||||||||||
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Title | Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Extended Active State | ||||||||||||
Map data | primary map | ||||||||||||
Sample |
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Function / homology | Function and homology information protein localization to pericentric heterochromatin / hepatocyte homeostasis / regulation of kidney development / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / [histone H3]-lysine27 N-trimethyltransferase / sex chromatin / negative regulation of keratinocyte differentiation / CAF-1 complex ...protein localization to pericentric heterochromatin / hepatocyte homeostasis / regulation of kidney development / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / [histone H3]-lysine27 N-trimethyltransferase / sex chromatin / negative regulation of keratinocyte differentiation / CAF-1 complex / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / ubiquitin-modified histone reader activity / random inactivation of X chromosome / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / regulatory ncRNA-mediated heterochromatin formation / response to tetrachloromethane / cerebellar cortex development / primary miRNA binding / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / facultative heterochromatin formation / negative regulation of cardiac muscle cell proliferation / positive regulation of cell cycle G1/S phase transition / 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 / RSC-type complex / protein-lysine N-methyltransferase activity / cardiac muscle hypertrophy in response to stress / negative regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex / pronucleus / Polo-like kinase mediated events / synaptic transmission, GABAergic / positive regulation of dendrite development / histone H3 methyltransferase activity / lncRNA binding / cardiac muscle cell proliferation / histone methyltransferase complex / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / G1 to G0 transition / negative regulation of gene expression, epigenetic / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / ATPase complex / histone methyltransferase activity / Sin3-type complex / negative regulation of transcription elongation by RNA polymerase II / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / negative regulation of cell differentiation / G0 and Early G1 / subtelomeric heterochromatin formation / negative regulation of cytokine production involved in inflammatory response / RNA polymerase II core promoter sequence-specific DNA binding / ribonucleoprotein complex binding / pericentric heterochromatin / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / positive regulation of epithelial to mesenchymal transition / Cyclin A:Cdk2-associated events at S phase entry / spleen development / keratinocyte differentiation / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / enzyme activator activity / protein localization to chromatin / methylated histone binding / B cell differentiation / SUMOylation of chromatin organization proteins / liver development / transcription corepressor binding / positive regulation of GTPase activity / thymus development / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of cell migration / PRC2 methylates histones and DNA / ubiquitin binding / cellular response to leukemia inhibitory factor / Regulation of PTEN gene transcription / Defective pyroptosis / stem cell differentiation / central nervous system development / hippocampus development / HDACs deacetylate histones / liver regeneration / promoter-specific chromatin binding / transcription coregulator activity / negative regulation of transforming growth factor beta receptor signaling pathway / brain development Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 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_7335.map.gz | 85.3 MB | EMDB map data format | |
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Header (meta data) | emd-7335-v30.xml emd-7335.xml | 26 KB 26 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7335_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_7335.png | 51 KB | ||
Others | emd_7335_half_map_1.map.gz emd_7335_half_map_2.map.gz | 71.4 MB 71.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7335 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7335 | HTTPS FTP |
-Validation report
Summary document | emd_7335_validation.pdf.gz | 820.1 KB | Display | EMDB validaton report |
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Full document | emd_7335_full_validation.pdf.gz | 819.7 KB | Display | |
Data in XML | emd_7335_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | emd_7335_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7335 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7335 | HTTPS FTP |
-Related structure data
Related structure data | 6c24MC 7334C 7337C 6c23C C: citing same article (ref.) M: atomic model generated by this map |
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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_7335.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_7335_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_7335_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: Protein Jumonji
+Macromolecule #4: Histone-lysine N-methyltransferase EZH2
+Macromolecule #5: Polycomb protein EED
+Macromolecule #6: Histone-binding protein RBBP4
+Macromolecule #7: JARID2-substrate
+Macromolecule #8: Zinc finger protein AEBP2
+Macromolecule #9: SUZ12
-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 |