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Yorodumi- PDB-5ij8: Structure of the primary oncogenic mutant Y641N Hs/AcPRC2 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ij8 | ||||||
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Title | Structure of the primary oncogenic mutant Y641N Hs/AcPRC2 in complex with a pyridone inhibitor | ||||||
Components |
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Keywords | transferase/transferase inhibitor / lysine methyltransferase / 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 / sex chromatin / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway ...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 / 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 / ESC/E(Z) complex / chromatin silencing 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 / positive regulation of dendrite development / histone H3 methyltransferase activity / lncRNA binding / SUMOylation of chromatin organization proteins / 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 / oligodendrocyte differentiation / negative regulation of transcription elongation by RNA polymerase II / Transcriptional Regulation by E2F6 / 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 / ribonucleoprotein complex binding / positive regulation of epithelial to mesenchymal transition / keratinocyte differentiation / protein localization to chromatin / enzyme activator activity / Regulation of PTEN gene transcription / methylated histone binding / liver regeneration / B cell differentiation / transcription corepressor binding / PRC2 methylates histones and DNA / positive regulation of MAP kinase activity / positive regulation of GTPase activity / Defective pyroptosis / stem cell differentiation / regulation of circadian rhythm / promoter-specific chromatin binding / hippocampus development / HCMV Early Events / PKMTs methylate histone lysines / protein modification process / positive regulation of protein serine/threonine kinase activity / G1/S transition of mitotic cell cycle / heterochromatin formation / chromatin DNA binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to hydrogen peroxide / rhythmic process / chromosome / transcription corepressor activity / chromatin organization / response to estradiol / chromosome, telomeric region / Oxidative Stress Induced Senescence / methylation / cell population proliferation / nuclear body / positive regulation of cell migration / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / synapse / chromatin / regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Anolis carolinensis (green anole) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Gajiwala, K.S. / Brooun, A. / Deng, Y.-L. / Liu, W. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Polycomb repressive complex 2 structure with inhibitor reveals a mechanism of activation and drug resistance. Authors: Brooun, A. / Gajiwala, K.S. / Deng, Y.L. / Liu, W. / Bolanos, B. / Bingham, P. / He, Y.A. / Diehl, W. / Grable, N. / Kung, P.P. / Sutton, S. / Maegley, K.A. / Yu, X. / Stewart, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ij8.cif.gz | 402.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ij8.ent.gz | 321.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ij8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ij8_validation.pdf.gz | 941.1 KB | Display | wwPDB validaton report |
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Full document | 5ij8_full_validation.pdf.gz | 972.3 KB | Display | |
Data in XML | 5ij8_validation.xml.gz | 64.2 KB | Display | |
Data in CIF | 5ij8_validation.cif.gz | 87.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/5ij8 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/5ij8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 72892.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anolis carolinensis (green anole), (gene. exp.) Homo sapiens (human) Gene: EZH2, EZH2, KMT6 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: G1KPH4, UniProt: Q15910, histone-lysine N-methyltransferase #2: Protein | Mass: 41776.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75530 #3: Protein | Mass: 22268.748 Da / Num. of mol.: 2 / Mutation: Y641N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUZ12, CHET9, JJAZ1, KIAA0160 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15022 #4: Chemical | #5: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.23 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 24.0 %w/v PEG monomethyl ether 2000, 0.0050 M TCEP hydrochloride, 0.1 M MES (pH 5.80) |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→115.13 Å / Num. obs: 49287 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 85 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.98→3.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→91.28 Å / Cor.coef. Fo:Fc: 0.9138 / Cor.coef. Fo:Fc free: 0.8697 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.387
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Displacement parameters | Biso mean: 69.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.374 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.99→91.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.99→3.07 Å / Total num. of bins used: 20
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