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- PDB-5hyn: Structure of Human Polycomb Repressive Complex 2 (PRC2) with onco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hyn | ||||||
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Title | Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide | ||||||
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![]() | TRANSFERASE / chromatin modification complex | ||||||
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 / sex chromatin / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity ...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 / 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 / chromatin silencing complex / ESC/E(Z) complex / protein-lysine N-methyltransferase activity / negative regulation of stem cell differentiation / RSC-type complex / pronucleus / cardiac muscle hypertrophy in response to stress / synaptic transmission, GABAergic / lncRNA binding / positive regulation of dendrite development / histone H3 methyltransferase activity / cardiac muscle cell proliferation / histone methyltransferase complex / negative regulation of gene expression, epigenetic / G1 to G0 transition / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / histone methyltransferase activity / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / negative regulation of transcription elongation by RNA polymerase II / negative regulation of cell differentiation / subtelomeric heterochromatin formation / negative regulation of cytokine production involved in inflammatory response / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / Chromatin modifying enzymes / ribonucleoprotein complex binding / heterochromatin formation / positive regulation of epithelial to mesenchymal transition / epigenetic regulation of gene expression / nucleosome binding / keratinocyte differentiation / enzyme activator activity / spleen development / protein localization to chromatin / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / B cell differentiation / DNA methylation / Condensation of Prophase Chromosomes / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / positive regulation of GTPase activity / thymus development / liver development / PRC2 methylates histones and DNA / cellular response to leukemia inhibitory factor / Regulation of PTEN gene transcription / ubiquitin binding / Defective pyroptosis / central nervous system development / HDACs deacetylate histones / liver regeneration / stem cell differentiation / hippocampus development / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / positive regulation of MAP kinase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / protein modification process / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / positive regulation of protein serine/threonine kinase activity / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / regulation of circadian rhythm / chromatin DNA binding / PKMTs methylate histone lysines Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Justin, N. / Wilson, J.R. / Gamblin, S.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2. Authors: Justin, N. / Zhang, Y. / Tarricone, C. / Martin, S.R. / Chen, S. / Underwood, E. / De Marco, V. / Haire, L.F. / Walker, P.A. / Reinberg, D. / Wilson, J.R. / Gamblin, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.7 MB | Display | ![]() |
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PDB format | ![]() | 1.4 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 163.8 KB | Display | |
Data in CIF | ![]() | 217.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
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Components
-Protein , 1 types, 4 molecules AFKQ
#1: Protein | Mass: 85492.297 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q15910, histone-lysine N-methyltransferase |
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-Polycomb protein ... , 2 types, 8 molecules BGLRCHMS
#2: Protein | Mass: 42314.145 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 15249.510 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein/peptide , 2 types, 8 molecules DIOTEJPU
#4: Protein/peptide | Mass: 1234.426 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() #5: Protein/peptide | Mass: 1505.743 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 2 types, 36 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/SAH.gif)
#6: Chemical | ChemComp-ZN / #7: Chemical | ChemComp-SAH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350, 400mM Ammonian Citrate pH6.5 / PH range: 6.5-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→104.43 Å / Num. obs: 132394 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.165 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.94→3.02 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.607 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→95.013 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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