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Open data
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Basic information
Entry | Database: PDB / ID: 5h17 | ||||||
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Title | EED in complex with PRC2 allosteric inhibitor EED210 | ||||||
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![]() | Transferase/Transferase Inhibitor / EED / PRC2 / inhibitor / Transferase-Transferase Inhibitor complex | ||||||
Function / homology | ![]() 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 / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / primary miRNA binding ...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 / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / primary miRNA binding / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / response to tetrachloromethane / cerebellar cortex development / facultative heterochromatin formation / histone H3K27 methyltransferase activity / 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 / pronucleus / cardiac muscle hypertrophy in response to stress / synaptic transmission, GABAergic / lncRNA binding / positive regulation of dendrite development / histone H3 methyltransferase activity / negative regulation of gene expression, epigenetic / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / G1 to G0 transition / histone methyltransferase activity / Transcriptional Regulation by E2F6 / negative regulation of transcription elongation by RNA polymerase II / 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 / heterochromatin formation / positive regulation of epithelial to mesenchymal transition / nucleosome binding / keratinocyte differentiation / protein localization to chromatin / enzyme activator activity / B cell differentiation / transcription corepressor binding / positive regulation of GTPase activity / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / stem cell differentiation / liver regeneration / hippocampus development / promoter-specific chromatin binding / positive regulation of MAP kinase activity / protein modification process / positive regulation of protein serine/threonine kinase activity / regulation of circadian rhythm / chromatin DNA binding / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to hydrogen peroxide / HCMV Early Events / G1/S transition of mitotic cell cycle / transcription corepressor activity / rhythmic process / response to estradiol / chromatin organization / chromosome / methylation / Oxidative Stress Induced Senescence / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / synapse / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, K. / Zhao, M. / Luo, X. / Zhang, H. | ||||||
![]() | ![]() Title: Discovery and Molecular Basis of a Diverse Set of Polycomb Repressive Complex 2 Inhibitors Recognition by EED Authors: Li, L. / Zhang, H. / Zhang, M. / Zhao, M. / Feng, L. / Luo, X. / Gao, Z. / Huang, Y. / Ardayfio, O. / Zhang, J.H. / Lin, Y. / Fan, H. / Mi, Y. / Li, G. / Liu, L. / Feng, L. / Luo, F. / Teng, ...Authors: Li, L. / Zhang, H. / Zhang, M. / Zhao, M. / Feng, L. / Luo, X. / Gao, Z. / Huang, Y. / Ardayfio, O. / Zhang, J.H. / Lin, Y. / Fan, H. / Mi, Y. / Li, G. / Liu, L. / Feng, L. / Luo, F. / Teng, L. / Qi, W. / Ottl, J. / Lingel, A. / Bussiere, D.E. / Yu, Z. / Atadja, P. / Lu, C. / Li, E. / Gu, J. / Zhao, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.9 KB | Display | ![]() |
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PDB format | ![]() | 70.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 768.7 KB | Display | ![]() |
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Full document | ![]() | 770.4 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5h13C ![]() 5h14C ![]() 5h15C ![]() 5h19C ![]() 2qxvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42356.246 Da / Num. of mol.: 1 / Fragment: UNP residues 76-441 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 3622.164 Da / Num. of mol.: 1 / Fragment: UNP residues 40-68 / Source method: obtained synthetically / Source: (synth.) ![]() References: UniProt: Q15910, histone-lysine N-methyltransferase |
#3: Chemical | ChemComp-LQE / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris, 16% PEG 8000,10 mM beta-Nicotinamide mononucleotide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979112 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 21839 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.274→2.281 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QXV Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.9174 / Cor.coef. Fo:Fc free: 0.8892 / SU R Cruickshank DPI: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.332 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.226
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Displacement parameters | Biso max: 126.88 Å2 / Biso mean: 42.38 Å2 / Biso min: 13.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.273 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.42 Å / Total num. of bins used: 10
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