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Yorodumi- PDB-5lv5: Crystal structure of mouse PRMT6 in complex with inhibitor LH1458 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lv5 | ||||||
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Title | Crystal structure of mouse PRMT6 in complex with inhibitor LH1458 | ||||||
Components | Protein arginine N-methyltransferase 6 | ||||||
Keywords | TRANSFERASE / S-ADENOSYL-L-METHIONINE | ||||||
Function / homology | Function and homology information histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / protein modification process / cellular senescence / histone binding / methylation / chromatin remodeling / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å | ||||||
Authors | Cura, V. / Marechal, N. / Troffer-Charlier, N. / Halby, L. / Arimondo, P. / Bonnefond, L. / Cavarelli, J. | ||||||
Citation | Journal: Philos. Trans. R. Soc. Lond., B, Biol. Sci. / Year: 2018 Title: Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors. Authors: Halby, L. / Marechal, N. / Pechalrieu, D. / Cura, V. / Franchini, D.M. / Faux, C. / Alby, F. / Troffer-Charlier, N. / Kudithipudi, S. / Jeltsch, A. / Aouadi, W. / Decroly, E. / Guillemot, J. ...Authors: Halby, L. / Marechal, N. / Pechalrieu, D. / Cura, V. / Franchini, D.M. / Faux, C. / Alby, F. / Troffer-Charlier, N. / Kudithipudi, S. / Jeltsch, A. / Aouadi, W. / Decroly, E. / Guillemot, J.C. / Page, P. / Ferroud, C. / Bonnefond, L. / Guianvarc'h, D. / Cavarelli, J. / Arimondo, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lv5.cif.gz | 200.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lv5.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 5lv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/5lv5 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/5lv5 | HTTPS FTP |
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-Related structure data
Related structure data | 5lv2C 5lv3C 5lv4C 5tbhC 5tbiC 5tbjC 4c07S 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: 44597.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt6, Hrmt1l6 / Production host: Escherichia coli (E. coli) References: UniProt: Q6NZB1, type I protein arginine methyltransferase |
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#2: Chemical | ChemComp-78G / |
#3: 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: 1.99 Å3/Da / Density % sol: 38.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris-HCl pH 8.0 100 mM PEG 6000 10 % MgCl2 200 mM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40.16 Å / Num. obs: 32113 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 23.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.261 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.421 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C07 Resolution: 1.802→40.16 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 19.89 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.802→40.16 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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