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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21707 | |||||||||
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Title | PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome | |||||||||
![]() | half map-1 for 2:1 | |||||||||
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Function / homology | ![]() 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 / regulatory ncRNA-mediated heterochromatin formation / sex chromatin / CAF-1 complex ...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 / regulatory ncRNA-mediated heterochromatin formation / 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 / 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 / negative regulation of cardiac muscle cell proliferation / positive regulation of cell cycle G1/S phase transition / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / 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 / NuRD complex / ESC/E(Z) complex / protein-lysine N-methyltransferase activity / negative regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex / pronucleus / RSC-type complex / cardiac muscle hypertrophy in response to stress / Polo-like kinase mediated events / synaptic transmission, GABAergic / lncRNA binding / positive regulation of dendrite development / histone H3 methyltransferase activity / cardiac muscle cell proliferation / histone methyltransferase complex / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of gene expression, epigenetic / spinal cord development / G1 to G0 transition / Sin3-type complex / histone methyltransferase activity / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / ATPase complex / 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 / 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 / pericentric heterochromatin / ribonucleoprotein complex binding / positive regulation of epithelial to mesenchymal transition / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / nucleosome binding / Maturation of protein E / keratinocyte differentiation / Maturation of protein E / Deposition of new CENPA-containing nucleosomes at the centromere / ER Quality Control Compartment (ERQC) / heterochromatin formation / spleen development / Myoclonic epilepsy of Lafora / protein localization to chromatin / FLT3 signaling by CBL mutants / enzyme activator activity / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of TP53 Activity through Acetylation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / methylated histone binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Kasinath V / Nogales E / Beck C / Sauer P / Poepsel S / Kosmatka J / Faini M / Toso D / Aebersold R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications. Authors: Vignesh Kasinath / Curtis Beck / Paul Sauer / Simon Poepsel / Jennifer Kosmatka / Marco Faini / Daniel Toso / Ruedi Aebersold / Eva Nogales / ![]() ![]() ![]() Abstract: Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) cooperate to determine cell identity by epigenetic gene expression regulation. However, the mechanism of PRC2 recruitment by means of recognition ...Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) cooperate to determine cell identity by epigenetic gene expression regulation. However, the mechanism of PRC2 recruitment by means of recognition of PRC1-mediated H2AK119ub1 remains poorly understood. Our PRC2 cryo-electron microscopy structure with cofactors JARID2 and AEBP2 bound to a H2AK119ub1-containing nucleosome reveals a bridge helix in EZH2 that connects the SET domain, H3 tail, and nucleosomal DNA. JARID2 and AEBP2 each interact with one ubiquitin and the H2A-H2B surface. JARID2 stimulates PRC2 through interactions with both the polycomb protein EED and the H2AK119-ubiquitin, whereas AEBP2 has an additional scaffolding role. The presence of these cofactors partially overcomes the inhibitory effect that H3K4me3 and H3K36me3 exert on core PRC2 (in the absence of cofactors). Our results support a key role for JARID2 and AEBP2 in the cross-talk between histone modifications and PRC2 activity. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 124.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 58.2 KB 58.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.6 KB | Display | ![]() |
Images | ![]() | 117.7 KB | ||
Masks | ![]() ![]() | 216 MB 216 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 125 MB 190.1 MB 189.9 MB 124.5 MB 149 MB 148.8 MB 149.1 MB 148.7 MB 124.4 MB 124.8 MB 171.4 MB 171 MB 171 MB 170.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 695.8 KB | Display | ![]() |
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Full document | ![]() | 695.4 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wkrMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | half map-1 for 2:1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1492 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Mask #2
+Additional map: local res filtered map 2:1 (Bfac = 50)
+Additional map: data set 2 half 1
+Additional map: data set 2 half 2
+Additional map: data set 2 loc res filtered (bfac 50)
+Additional map: body 1 half map 1 multibody
+Additional map: body 2 half map 1 multibody
+Additional map: body 1 half map 2 multibody
+Additional map: body 2 half map 2 multibody
+Additional map: body 1 local res filtered (Bfac = 50)
+Additional map: body 2 local res filtered (Bfac = 50)
+Additional map: half map-1 for 2:1
+Additional map: half map-2 for 2:1
+Half map: half map 1 full refined map
+Half map: data set 2 half 1
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Sample components
+Entire : PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome
+Supramolecule #1: PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome
+Supramolecule #2: PRC2-AEBP2-JARID2
+Supramolecule #3: H2AK119ub1 nucleosome
+Macromolecule #1: Ubiquitin
+Macromolecule #2: Polycomb protein SUZ12
+Macromolecule #3: Polycomb protein EED
+Macromolecule #4: Histone-binding protein RBBP4
+Macromolecule #5: Histone-lysine N-methyltransferase EZH2
+Macromolecule #6: Protein Jumonji
+Macromolecule #7: Zinc finger protein AEBP2
+Macromolecule #9: Histone H3.2
+Macromolecule #10: Histone H4
+Macromolecule #11: Histone H2A type 1
+Macromolecule #12: Histone H2B 1.1
+Macromolecule #8: DNA (314-MER)
+Macromolecule #13: MAGNESIUM ION
+Macromolecule #14: S-ADENOSYL-L-HOMOCYSTEINE
+Macromolecule #15: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |