+Open data
-Basic information
Entry | Database: PDB / ID: 6sqk | ||||||
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Title | Crystal structure of mouse PRMT6 with modified H7-4 peptide | ||||||
Components |
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Keywords | TRANSFERASE / SAM binding domain / arginine methylation | ||||||
Function / homology | Function and homology information histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity ...histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 H3 methyltransferase activity / 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 / 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) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Bonnefond, L. / Cavarelli, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of mouse PRMT6 in complex with inhibitors Authors: Bonnefond, L. / Cavarelli, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sqk.cif.gz | 391.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sqk.ent.gz | 325.7 KB | Display | PDB format |
PDBx/mmJSON format | 6sqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/6sqk ftp://data.pdbj.org/pub/pdb/validation_reports/sq/6sqk | HTTPS FTP |
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-Related structure data
Related structure data | 6sq3C 6sq4C 6sqhC 6sqiC 4c03S 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: 42077.523 Da / Num. of mol.: 2 / Mutation: F315L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt6, Hrmt1l6 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q6NZB1, type I protein arginine methyltransferase #2: Protein/peptide | Mass: 879.946 Da / Num. of mol.: 2 / Mutation: R4(URG) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: histone-lysine N-methyltransferase #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3,350 20%, Mg(CH3COO)2 200 mM, HEPES-NaOH pH 7.0 100 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→47.61 Å / Num. obs: 140415 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.039 / Rrim(I) all: 0.14 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 12.7 % / Rmerge(I) obs: 2.523 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 13708 / CC1/2: 0.395 / Rpim(I) all: 0.734 / Rrim(I) all: 2.629 / % possible all: 98.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4c03 Resolution: 1.4→45.629 Å / Cross valid method: THROUGHOUT / σ(F): 1.35
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Displacement parameters | Biso max: 100.21 Å2 / Biso mean: 27.3722 Å2 / Biso min: 11.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→45.629 Å
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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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