+Open data
-Basic information
Entry | Database: PDB / ID: 5kkl | ||||||
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Title | Structure of ctPRC2 in complex with H3K27me3 and H3K27M | ||||||
Components |
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Keywords | TRANSFERASE / Complex / Methyltransferase / Histone H3 | ||||||
Function / homology | Function and homology information histone methyltransferase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events ...histone methyltransferase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / methylation / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å | ||||||
Authors | Jiao, L. / Liu, X. | ||||||
Citation | Journal: Science / Year: 2016 Title: Response to Comment on "Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2". Authors: Jiao, L. / Liu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kkl.cif.gz | 563.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kkl.ent.gz | 458 KB | Display | PDB format |
PDBx/mmJSON format | 5kkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/5kkl ftp://data.pdbj.org/pub/pdb/validation_reports/kk/5kkl | HTTPS FTP |
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-Related structure data
Related structure data | 5kjhSC 5kjiC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 66021.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0029920 / Production host: Saccharomyces cerevisiae S288c (yeast) / References: UniProt: G0S8H7 | ||
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#2: Protein | Mass: 106890.555 Da / Num. of mol.: 1 / Mutation: K2027M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus), (gene. exp.) Homo sapiens (human) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0053230 / Production host: Saccharomyces cerevisiae S288c (yeast) References: UniProt: G0SDW4, UniProt: P68431, UniProt: G0RYC6 | ||
#3: Protein/peptide | Mass: 1146.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS | ||
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-SAM / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15% PEG4000, 175mM ammonium citrate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→50 Å / Num. obs: 36440 / % possible obs: 98 % / Redundancy: 6.5 % / Biso Wilson estimate: 65.81 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Net I/σ(I): 24.15 |
Reflection shell | Resolution: 2.94→3 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 1739 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KJH Resolution: 2.94→48.74 Å / Cor.coef. Fo:Fc: 0.8784 / Cor.coef. Fo:Fc free: 0.8319 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.41
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Displacement parameters | Biso mean: 78.88 Å2
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Refine analyze | Luzzati coordinate error obs: 0.351 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.94→48.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.94→3.04 Å / Total num. of bins used: 16
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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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