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- PDB-3hna: Crystal structure of catalytic domain of human euchromatic histon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hna | ||||||
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Title | Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and mono-Methylated H3K9 Peptide | ||||||
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![]() | HYDROLASE/HYDROLASE REGULATOR / EHMT1 / Structural Genomics / sgc / Structural Genomics Consortium / ANK repeat / Chromatin regulator / Metal-binding / Methyltransferase / Nucleus / Phosphoprotein / S-adenosyl-L-methionine / Transferase / HYDROLASE-HYDROLASE REGULATOR COMPLEX | ||||||
Function / homology | ![]() [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / DNA methylation-dependent heterochromatin formation / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / Transcriptional Regulation by E2F6 ...[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / DNA methylation-dependent heterochromatin formation / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / Transcriptional Regulation by E2F6 / regulation of embryonic development / Transcriptional Regulation by VENTX / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / transcription corepressor binding / methyltransferase activity / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / chromatin organization / positive regulation of cold-induced thermogenesis / Senescence-Associated Secretory Phenotype (SASP) / nuclear body / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Min, J. / Wu, H. / Loppnau, P. / Wleigelt, 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 | ![]() | 151.6 KB | Display | ![]() |
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PDB format | ![]() | 114.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 51 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2igqC ![]() 2o8jC ![]() 2qpwC ![]() 2r3aC ![]() 2rfiSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Components
#1: Protein | Mass: 32974.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9H9B1, histone-lysine N-methyltransferase #2: Protein/peptide | Mass: 1264.455 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.14 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20%PEG3350, pH 6.0, 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: Jan 1, 2007 / Details: v |
Radiation | Monochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→100 Å / Num. all: 101405 / Num. obs: 101405 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 12 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2RFI Resolution: 1.5→62.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.049 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.068 / 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: 17.872 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→62.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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