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Yorodumi- PDB-6sqi: Crystal structure of mouse PRMT6 with C-terminal TEV cleavage site -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sqi | ||||||
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Title | Crystal structure of mouse PRMT6 with C-terminal TEV cleavage site | ||||||
Components | Protein arginine N-methyltransferase 6 | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 | 6sqi.cif.gz | 201.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sqi.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 6sqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/6sqi ftp://data.pdbj.org/pub/pdb/validation_reports/sq/6sqi | HTTPS FTP |
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-Related structure data
Related structure data | 6sq3C 6sq4C 6sqhC 6sqkC 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: 42821.301 Da / Num. of mol.: 1 / Fragment: mouse PRMT6 / Mutation: F315L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt6, Hrmt1l6 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q6NZB1, type I protein arginine methyltransferase |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.79 % / Mosaicity: 0.11 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: PEG Smear High 8%, NaCHOO 40 mM, CaCl2 40 mM, PIPES pH 6.8 100 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.16 |
Reflection | Resolution: 1.6→40.69 Å / Num. obs: 47624 / % possible obs: 99 % / Redundancy: 8.6 % / Biso Wilson estimate: 19.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.016 / Rrim(I) all: 0.052 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2048 / CC1/2: 0.436 / Rpim(I) all: 0.529 / Rrim(I) all: 0.913 / % possible all: 85.2 |
-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: 1.6→40.69 Å / Cross valid method: THROUGHOUT / σ(F): 1.33
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Displacement parameters | Biso max: 97.84 Å2 / Biso mean: 26.7729 Å2 / Biso min: 12.21 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→40.69 Å
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Refinement TLS params. | Method: refined / Origin x: 21.2622 Å / Origin y: 1.4764 Å / Origin z: 8.3403 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 52 through 386) |