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Open data
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Basic information
Entry | Database: PDB / ID: 2o8j | ||||||
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Title | Human euchromatic histone methyltransferase 2 | ||||||
![]() | Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 | ||||||
![]() | TRANSFERASE / HLA-B-associated transcript 8 / BAT8 / G9a / NG36/G9a / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 / long-term memory / response to fungicide / cellular response to starvation / Transferases; Transferring one-carbon groups; Methyltransferases / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / cellular response to xenobiotic stimulus / Senescence-Associated Secretory Phenotype (SASP) / response to ethanol / nuclear speck / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Min, J. / Wu, H. / Antoshenko, T. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structural biology of human H3K9 methyltransferases Authors: Wu, H. / Min, J. / Lunin, V.V. / Antoshenko, T. / Dombrovski, L. / Zeng, H. / Allali-Hassani, A. / Campagna-Slater, V. / Vedadi, M. / Arrowsmith, C.H. / Plotnikov, A.N. / Schapira, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.4 KB | Display | ![]() |
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PDB format | ![]() | 196 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 51.3 KB | Display | |
Data in CIF | ![]() | 75.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2igqSC ![]() 2qpwC ![]() 2r3aC ![]() 2rfiC ![]() 3hnaC S: Starting model for refinement C: citing same article ( |
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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: 32460.799 Da / Num. of mol.: 4 / Fragment: residues 913-1193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96KQ7, histone-lysine N-methyltransferase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SAH / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.83 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: peg 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→79.3 Å / Num. all: 100323 / Num. obs: 100323 / % possible obs: 92.23 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IGQ Resolution: 1.8→79.31 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.395 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.168 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→79.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20
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