+Open data
-Basic information
Entry | Database: PDB / ID: 4j7f | ||||||
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Title | SET7/9Y335pAF in complex with TAF10 peptide and AdoHcy | ||||||
Components |
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Keywords | TRANSFERASE/PEPTIDE / SET domain / lysine methyltransferase / Y335pAF mutation / TRANSFERASE-PEPTIDE complex | ||||||
Function / homology | Function and homology information heterochromatin organization / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / transcription factor TFTC complex / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / hepatocyte differentiation ...heterochromatin organization / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / transcription factor TFTC complex / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / hepatocyte differentiation / protein-lysine N-methyltransferase activity / SAGA complex / RNA polymerase binding / limb development / histone H3 methyltransferase activity / transcription preinitiation complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / histone methyltransferase activity / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / regulation of RNA splicing / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / regulation of DNA repair / somitogenesis / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / male germ cell nucleus / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / G1/S transition of mitotic cell cycle / multicellular organism growth / mRNA transcription by RNA polymerase II / PKMTs methylate histone lysines / p53 binding / chromosome / chromatin organization / HATs acetylate histones / response to ethanol / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / Ub-specific processing proteases / chromatin remodeling / apoptotic process / DNA damage response / chromatin binding / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / enzyme binding / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Horowitz, S. / Del Rizzo, P.A. / Trievel, R.C. | ||||||
Citation | Journal: To be Published Title: Methyl CH O Hydrogen Bonds Orchestrate AdoMet-Dependent Methylation Authors: Horowitz, S. / Dirk, L.M.A. / Yesselman, J.D. / Nimtz, J.S. / Del Rizzo, P.A. / Vander Meulen, K.A. / Butcher, S.E. / Mehl, R.A. / Houtz, R.L. / Al-Hashimi, H.M. / Trievel, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j7f.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j7f.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 4j7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/4j7f ftp://data.pdbj.org/pub/pdb/validation_reports/j7/4j7f | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 29042.346 Da / Num. of mol.: 1 / Mutation: Y335pAF Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETD7, KIAA1717, KMT7, SET7, SET9 / Production host: Escherichia coli (E. coli) References: UniProt: Q8WTS6, histone-lysine N-methyltransferase |
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#2: Protein/peptide | Mass: 1255.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetically produced peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12962 |
#3: Chemical | ChemComp-SAH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.81 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Sodium citrate, imidazole, nickel chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→71.92 Å / Num. all: 51202 / Num. obs: 48193 |
Reflection shell | Resolution: 1.6→1.64 Å / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→71.92 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.434 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.074 / 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: 23.915 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→71.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.595→1.636 Å / Total num. of bins used: 20
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