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Yorodumi- PDB-5t0m: A histone H3K9M mutation traps histone methyltransferase Clr4 to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t0m | |||||||||||||||
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Title | A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading | |||||||||||||||
Components |
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Keywords | TRANSFERASE / histone methyltransferase / SET domain | |||||||||||||||
Function / homology | Function and homology information regulation of protein modification process / histone H3K56 methyltransferase activity / : / phenotypic switching / neuron fate specification / : / [histone H3]-lysine9 N-methyltransferase / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity ...regulation of protein modification process / histone H3K56 methyltransferase activity / : / phenotypic switching / neuron fate specification / : / [histone H3]-lysine9 N-methyltransferase / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / synaptonemal complex assembly / negative regulation of autophagosome assembly / protein-lysine N-methyltransferase activity / oocyte development / C2H2 zinc finger domain binding / fertilization / : / cellular response to cocaine / : / organ growth / Transcriptional Regulation by E2F6 / spermatid development / behavioral response to cocaine / regulation of DNA replication / RNA Polymerase I Transcription Initiation / Transcriptional Regulation by VENTX / long-term memory / Chromatin modifying enzymes / epigenetic regulation of gene expression / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to starvation / 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 / transcription corepressor binding / 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 / promoter-specific chromatin binding / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / Regulation of TP53 Activity through Methylation / 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 / cellular response to xenobiotic stimulus / p53 binding / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / response to ethanol / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nuclear speck / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 Å | |||||||||||||||
Authors | Xu, K. / Tong, L. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Elife / Year: 2016 Title: A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading. Authors: Shan, C.M. / Wang, J. / Xu, K. / Chen, H. / Yue, J.X. / Andrews, S. / Moresco, J.J. / Yates, J.R. / Nagy, P.L. / Tong, L. / Jia, S. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t0m.cif.gz | 138.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t0m.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 5t0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/5t0m ftp://data.pdbj.org/pub/pdb/validation_reports/t0/5t0m | HTTPS FTP |
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-Related structure data
Related structure data | 5t0kC 2o8jS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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
-Protein / Protein/peptide , 2 types, 4 molecules ABPC
#1: Protein | Mass: 32460.799 Da / Num. of mol.: 2 / Fragment: unp residues 879-1159 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 / Production host: Escherichia coli (E. coli) References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase #2: Protein/peptide | Mass: 1549.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS |
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-Non-polymers , 4 types, 363 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-SAH / | #6: Water | ChemComp-HOH / | |
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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: 2.34 Å3/Da / Density % sol: 47.42 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris propane (pH 7.5), 18% (w/v) PEG3350, 0.2 M NaF, and 5% (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 49342 / % possible obs: 99.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 37.1 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5.8 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O8J Resolution: 1.896→44.897 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.896→44.897 Å
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Refine LS restraints |
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LS refinement shell |
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