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- PDB-5jj0: Structure of G9a SET-domain with Histone H3K9M peptide and excess SAH -
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Basic information
Entry | Database: PDB / ID: 5jj0 | ||||||
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Title | Structure of G9a SET-domain with Histone H3K9M peptide and excess SAH | ||||||
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![]() | TRANSFERASE / SET-domain / Histone methyl transferase / histone peptide | ||||||
Function / homology | ![]() 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 / DNA methylation-dependent heterochromatin formation / oocyte development / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / fertilization / 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 / Chromatin modifying enzymes / long-term memory / epigenetic regulation of gene expression / response to fungicide / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / cellular response to starvation / Assembly of the ORC complex at the origin of replication / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / Condensation of Prophase Chromosomes / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Formation of the beta-catenin:TCF transactivating complex / 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 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / p53 binding / cellular response to xenobiotic stimulus / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jayaram, H. / Bellon, S.F. / Poy, F. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132 KB | Display | ![]() |
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PDB format | ![]() | 101 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jhnC ![]() 5jinC ![]() 5jiyC ![]() 2o8jS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31661.904 Da / Num. of mol.: 2 Fragment: SET domain of Histone-lysine N-methyltransferase EHMT2 G9a, UNP residues 882-1155 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase #2: Protein/peptide | Mass: 1139.284 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M Tri-ammonium citrate pH 7 and 20% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 178 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.001 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→45.91 Å / Num. obs: 63270 / % possible obs: 98.73 % / Redundancy: 3.6 % / Net I/σ(I): 10.13 |
Reflection shell | Resolution: 1.72→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2.2 / % possible all: 87.49 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2O8J Resolution: 1.72→45.91 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.309 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.121 / 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: 31.777 Å2
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Refinement step | Cycle: 1 / Resolution: 1.72→45.91 Å
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