+Open data
-Basic information
Entry | Database: PDB / ID: 3m58 | ||||||
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Title | SET7/9 Y245A in complex with TAF10-K189me1 peptide and AdoHcy | ||||||
Components |
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Keywords | TRANSFERASE / TERNARY COMPLEX / SET DOMAIN / METHYLTRANSFERASE / S-ADENOSYL-L-HOMOCYSTEINE / TAF10 PEPTIDE / N-MONOMETHYLLYSINE / Chromatin regulator / Chromosomal protein / S-adenosyl-L-methionine / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information 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 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 / RNA polymerase binding / histone H3 methyltransferase activity / SAGA complex / limb development / transcription preinitiation 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 / transcription factor TFIID complex / heterochromatin organization / RNA polymerase II general transcription initiation factor activity / 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 / DNA-templated transcription initiation / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / mRNA transcription by RNA polymerase II / multicellular organism growth / G1/S transition of mitotic cell cycle / 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 / regulation of DNA-templated transcription / nucleolus / 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 / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Del Rizzo, P.A. / Couture, J.-F. / Roiko, M.S. / Strunk, B.S. / Brunzelle, J.S. / Dirk, L.M. / Houtz, R.L. / Trievel, R.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation. Authors: Del Rizzo, P.A. / Couture, J.F. / Dirk, L.M. / Strunk, B.S. / Roiko, M.S. / Brunzelle, J.S. / Houtz, R.L. / 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 | 3m58.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m58.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 3m58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/3m58 ftp://data.pdbj.org/pub/pdb/validation_reports/m5/3m58 | HTTPS FTP |
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-Related structure data
Related structure data | 3m53C 3m54C 3m55C 3m56C 3m57C 3m59C 3m5aC 2f69S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28951.236 Da / Num. of mol.: 1 / Fragment: UNP residues 110-366 / Mutation: Y245A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: 9606 / Gene: KIAA1717, KMT7, SET7, SET9, SETD7 / Plasmid: pHIS2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2 References: UniProt: Q8WTS6, histone-lysine N-methyltransferase | ||
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#2: Protein/peptide | Mass: 1268.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12962*PLUS | ||
#3: Chemical | ChemComp-SAH / | ||
#4: Chemical | #5: 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: 3.15 Å3/Da / Density % sol: 60.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.9 M Ammonium Sulfate, 0.1 M Bis-Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0093 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→35 Å / Num. obs: 74675 / % possible obs: 98.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 22.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2F69 Resolution: 1.4→33.71 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.485 / SU ML: 0.027 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.053 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.007 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→33.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.435 Å / Total num. of bins used: 20
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