+Open data
-Basic information
Entry | Database: PDB / ID: 5h17 | ||||||
---|---|---|---|---|---|---|---|
Title | EED in complex with PRC2 allosteric inhibitor EED210 | ||||||
Components |
| ||||||
Keywords | Transferase/Transferase Inhibitor / EED / PRC2 / inhibitor / Transferase-Transferase Inhibitor complex | ||||||
Function / homology | Function and homology information 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 / 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 / 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 / positive regulation of dendrite development / histone H3 methyltransferase activity / lncRNA binding / negative regulation of G1/S transition of mitotic cell cycle / G1 to G0 transition / negative regulation of gene expression, epigenetic / spinal cord development / histone methyltransferase activity / negative regulation of transcription elongation by RNA polymerase II / Transcriptional Regulation by E2F6 / 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 / 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 / promoter-specific chromatin binding / hippocampus development / liver regeneration / positive regulation of MAP kinase activity / protein modification process / positive regulation of protein serine/threonine kinase activity / regulation of circadian rhythm / heterochromatin formation / 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 / Oxidative Stress Induced Senescence / methylation / chromosome, telomeric region / positive regulation of cell migration / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Zhao, K. / Zhao, M. / Luo, X. / Zhang, H. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5h17.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5h17.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 5h17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/5h17 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/5h17 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5h13C 5h14C 5h15C 5h19C 2qxvS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Gene: EED / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / References: UniProt: O75530 |
---|---|
#2: Protein/peptide | Mass: 3622.164 Da / Num. of mol.: 1 / Fragment: UNP residues 40-68 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q15910, histone-lysine N-methyltransferase |
#3: Chemical | ChemComp-LQE / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.27 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979112 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.88 Å2 / Biso mean: 42.38 Å2 / Biso min: 13.95 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.273 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.42 Å / Total num. of bins used: 10
|