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Open data
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Basic information
Entry | Database: PDB / ID: 3m59 | ||||||
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Title | SET7/9 Y245A in complex with TAF10-K189me2 peptide and AdoHcy | ||||||
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![]() | TRANSFERASE / TERNARY COMPLEX / SET DOMAIN / METHYLTRANSFERASE / S-ADENOSYL-L-HOMOCYSTEINE / TAF10 PEPTIDE / N-DIMETHYLLYSINE / Chromatin regulator / Chromosomal protein / Nucleus / S-adenosyl-L-methionine / Transcription / Transcription regulation | ||||||
Function / homology | ![]() 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 / histone H3 methyltransferase activity / RNA polymerase binding / 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 / RNA polymerase II general transcription initiation factor activity / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / regulation of DNA repair / somitogenesis / heterochromatin organization / 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 / PKMTs methylate histone lysines / G1/S transition of mitotic cell cycle / p53 binding / chromatin organization / chromosome / 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 / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.3 KB | Display | ![]() |
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PDB format | ![]() | 53.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 827.7 KB | Display | ![]() |
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Full document | ![]() | 828.3 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 21.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3m53C ![]() 3m54C ![]() 3m55C ![]() 3m56C ![]() 3m57C ![]() 3m58C ![]() 3m5aC ![]() 2f69S 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#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.) ![]() ![]() ![]() References: UniProt: Q8WTS6, histone-lysine N-methyltransferase |
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#2: Protein/peptide | Mass: 1282.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 245 molecules ![](data/chem/img/SAH.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SAH / | ||||
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#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 1.9 M Ammonium Sulfate, 0.1 M Bis-Tris pH 6.4, 0.005 M CoCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→40 Å / Num. obs: 40597 / % possible obs: 95 % / Redundancy: 6 % / Rmerge(I) obs: 0.055 / Χ2: 1.394 / Net I/σ(I): 15.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2F69 Resolution: 1.7→36.16 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.872 / SU B: 1.733 / SU ML: 0.057 / SU R Cruickshank DPI: 0.092 / SU Rfree: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 102.66 Å2 / Biso mean: 27.057 Å2 / Biso min: 11.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→36.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.747 Å / Total num. of bins used: 20
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