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Yorodumi- PDB-5cpr: The novel SUV4-20 inhibitor A-196 verifies a role for epigenetics... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cpr | ||||||
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Title | The novel SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity | ||||||
Components | Histone-lysine N-methyltransferase SUV420H1 | ||||||
Keywords | TRANSFERASE / protein lysine transferase / H4K20 / non-homologous end joining | ||||||
Function / homology | Function and homology information [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / positive regulation of isotype switching / condensed chromosome, centromeric region / S-adenosyl-L-methionine binding / muscle organ development ...[histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / positive regulation of isotype switching / condensed chromosome, centromeric region / S-adenosyl-L-methionine binding / muscle organ development / positive regulation of double-strand break repair via nonhomologous end joining / histone methyltransferase activity / PKMTs methylate histone lysines / methylation / DNA repair / chromatin binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Jakob, C.G. / Upadhyay, A.K. / Sun, C. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: The SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity. Authors: Bromberg, K.D. / Mitchell, T.R. / Upadhyay, A.K. / Jakob, C.G. / Jhala, M.A. / Comess, K.M. / Lasko, L.M. / Li, C. / Tuzon, C.T. / Dai, Y. / Li, F. / Eram, M.S. / Nuber, A. / Soni, N.B. / ...Authors: Bromberg, K.D. / Mitchell, T.R. / Upadhyay, A.K. / Jakob, C.G. / Jhala, M.A. / Comess, K.M. / Lasko, L.M. / Li, C. / Tuzon, C.T. / Dai, Y. / Li, F. / Eram, M.S. / Nuber, A. / Soni, N.B. / Manaves, V. / Algire, M.A. / Sweis, R.F. / Torrent, M. / Schotta, G. / Sun, C. / Michaelides, M.R. / Shoemaker, A.R. / Arrowsmith, C.H. / Brown, P.J. / Santhakumar, V. / Martin, A. / Rice, J.C. / Chiang, G.G. / Vedadi, M. / Barsyte-Lovejoy, D. / Pappano, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cpr.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cpr.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 5cpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cpr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5cpr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5cpr_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 5cpr_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/5cpr ftp://data.pdbj.org/pub/pdb/validation_reports/cp/5cpr | HTTPS FTP |
-Related structure data
Related structure data | 3s8pS 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: 30924.996 Da / Num. of mol.: 1 / Fragment: Set Domain residues 69-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUV420H1, KMT5B, CGI-85 / Production host: Escherichia coli (E. coli) References: UniProt: Q4FZB7, histone-lysine N-methyltransferase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SAM / |
#4: Chemical | ChemComp-539 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: The purified protein was concentrated to 10 mg/mL and with 1 mM SAM. SAM bound protein crystals were obtained by hanging drop vapor diffusion method at 17C using 10% (w/v) ethanol, 5% (w/v) ...Details: The purified protein was concentrated to 10 mg/mL and with 1 mM SAM. SAM bound protein crystals were obtained by hanging drop vapor diffusion method at 17C using 10% (w/v) ethanol, 5% (w/v) glycerol, 0.1 M tris pH 8.5 as the well solution. A-196 was soaked into the crystals |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.217→47.913 Å / Num. obs: 13537 / % possible obs: 99.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 34.06 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.217→2.225 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.018 / Mean I/σ(I) obs: 2.2 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S8P Resolution: 2.22→38.47 Å / Cor.coef. Fo:Fc: 0.9138 / Cor.coef. Fo:Fc free: 0.8876 / SU R Cruickshank DPI: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.296 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.214
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Displacement parameters | Biso mean: 37.52 Å2
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Refine analyze | Luzzati coordinate error obs: 0.268 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.22→38.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.4 Å / Total num. of bins used: 7
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