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Yorodumi- PDB-5jhn: Structure of G9a SET-domain with Histone H3K9Ala mutant peptide a... -
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-Basic information
Entry | Database: PDB / ID: 5jhn | ||||||
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Title | Structure of G9a SET-domain with Histone H3K9Ala mutant peptide and bound S-adenosylmethionine | ||||||
Components |
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Keywords | TRANSFERASE / SET-domain / Histone methyl transferase / histone peptide | ||||||
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 H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / synaptonemal complex assembly ...regulation of protein modification process / histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly / oocyte development / protein-lysine N-methyltransferase activity / fertilization / C2H2 zinc finger domain binding / DNA methylation-dependent heterochromatin formation / cellular response to cocaine / negative regulation of gene expression via chromosomal CpG island methylation / organ growth / Transcriptional Regulation by E2F6 / regulation of DNA replication / RNA Polymerase I Transcription Initiation / behavioral response to cocaine / Transcriptional Regulation by VENTX / spermatid development / telomere organization / long-term memory / Chromatin modifying enzymes / response to fungicide / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / cellular response to starvation / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Transferases; Transferring one-carbon groups; Methyltransferases / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription corepressor binding / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / Regulation of TP53 Activity through Methylation / p53 binding / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / cellular response to xenobiotic stimulus / nucleosome / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / Oxidative Stress Induced Senescence / response to ethanol / Estrogen-dependent gene expression / nuclear speck / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.67 Å | ||||||
Authors | Jayaram, H. / Bellon, S.F. / Poy, F. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: S-adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3. Authors: Jayaram, H. / Hoelper, D. / Jain, S.U. / Cantone, N. / Lundgren, S.M. / Poy, F. / Allis, C.D. / Cummings, R. / Bellon, S. / Lewis, P.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jhn.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jhn.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jhn_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5jhn_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5jhn_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 5jhn_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/5jhn ftp://data.pdbj.org/pub/pdb/validation_reports/jh/5jhn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 919 - 1188 / Label seq-ID: 4 - 273
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-Components
#1: Protein | Mass: 31661.904 Da / Num. of mol.: 2 / Fragment: UNP residues 882-1155 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) / Strain (production host): BL21(DE3) Rosetta References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase #2: Protein/peptide | Mass: 1079.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS #3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 2.49 Å3/Da / Density % sol: 50.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 0.2 M Tri-ammonium citrate pH 7 and 20% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 175 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.01 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→34.5 Å / Num. obs: 70175 / % possible obs: 99.19 % / Redundancy: 3.7 % / Net I/σ(I): 16.67 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.67→34.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.882 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.414 Å2
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Refinement step | Cycle: 1 / Resolution: 1.67→34.5 Å
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Refine LS restraints |
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