+Open data
-Basic information
Entry | Database: PDB / ID: 5eg2 | ||||||
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Title | SET7/9 N265A in complex with AdoHcy and TAF10 peptide | ||||||
Components |
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Keywords | Transferase/Transcription Factor / Transferase-Transcription Factor 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 / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Kroner, G.M. / Fick, R.J. / Trievel, R.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Sulfur-Oxygen Chalcogen Bonding Mediates AdoMet Recognition in the Lysine Methyltransferase SET7/9. Authors: Fick, R.J. / Kroner, G.M. / Nepal, B. / Magnani, R. / Horowitz, S. / Houtz, R.L. / Scheiner, S. / 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 | 5eg2.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eg2.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 5eg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/5eg2 ftp://data.pdbj.org/pub/pdb/validation_reports/eg/5eg2 | HTTPS FTP |
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-Related structure data
Related structure data | 4j83S S: Starting model for refinement |
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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: 29087.385 Da / Num. of mol.: 1 / Mutation: N265A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETD7, KIAA1717, KMT7, SET7, SET9 / Plasmid: pHIS2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 BL21(DE3) References: UniProt: Q8WTS6, histone-lysine N-methyltransferase |
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#2: Protein/peptide | Mass: 1242.446 Da / Num. of mol.: 1 / Fragment: UNP residues 186-195 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12962 |
#3: Chemical | ChemComp-SAH / |
#4: Chemical | ChemComp-NA / |
#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: 3.16 Å3/Da / Density % sol: 61.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 1:1 ratio of protein solution to crystallization solution. Protein solution: 4.0-8.0 mg/mL protein, 2.5 mM AdoMet, 2.0 mM TAF10 peptide, and 2.0 mM TCEP Crystallant solution: 0.99 - 1.02 M ...Details: 1:1 ratio of protein solution to crystallization solution. Protein solution: 4.0-8.0 mg/mL protein, 2.5 mM AdoMet, 2.0 mM TAF10 peptide, and 2.0 mM TCEP Crystallant solution: 0.99 - 1.02 M sodium citrate, 12 - 22 mM nickel (II) chloride, and 100 mM imidazole pH 8.4 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97903 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 10.9 % / Number: 612830 / Rmerge(I) obs: 0.068 / Χ2: 1 / D res high: 1.55 Å / D res low: 50 Å / Num. obs: 56195 / % possible obs: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.55→50 Å / Num. obs: 56195 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 19.16 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.022 / Rrim(I) all: 0.071 / Χ2: 1.005 / Net I/av σ(I): 34.59 / Net I/σ(I): 19.49 / Num. measured all: 612830 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J83 Resolution: 1.55→39.907 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.03 Å2 / Biso mean: 29.5651 Å2 / Biso min: 10.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→39.907 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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