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Yorodumi- PDB-4g56: Crystal Structure of full length PRMT5/MEP50 complexes from Xenop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g56 | ||||||
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Title | Crystal Structure of full length PRMT5/MEP50 complexes from Xenopus laevis | ||||||
Components |
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Keywords | TRANSFERASE / protein arginine methyltransferase / protein complexes / histone methylation / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC | ||||||
Function / homology | Function and homology information : / : / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / Golgi ribbon formation / histone arginine N-methyltransferase activity / methylosome / positive regulation of proteasomal protein catabolic process / mitotic DNA replication checkpoint signaling / histone methyltransferase complex ...: / : / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / Golgi ribbon formation / histone arginine N-methyltransferase activity / methylosome / positive regulation of proteasomal protein catabolic process / mitotic DNA replication checkpoint signaling / histone methyltransferase complex / regulation of mitotic nuclear division / E-box binding / circadian regulation of gene expression / transcription corepressor activity / cell division / Golgi apparatus / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Ho, M. / Wilczek, C. / Bonanno, J. / Shechter, D. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Structure of the arginine methyltransferase PRMT5-MEP50 reveals a mechanism for substrate specificity Authors: Ho, M.C. / Wilczek, C. / Bonanno, J.B. / Xing, L. / Seznec, J. / Matsui, T. / Carter, L.G. / Onikubo, T. / Kumar, P.R. / Chan, M.K. / Brenowitz, M. / Cheng, R.H. / Reimer, U. / Almo, S.C. / Shechter, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g56.cif.gz | 370 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g56.ent.gz | 305.3 KB | Display | PDB format |
PDBx/mmJSON format | 4g56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/4g56 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/4g56 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 75713.453 Da / Num. of mol.: 2 / Fragment: UNP residues 2-633 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hsl7, PRMT5 / Plasmid: pFL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q6NUA1 #2: Protein | Mass: 38872.746 Da / Num. of mol.: 2 / Fragment: UNP residues 2-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: MEP50, MGC81050, wdr77 / Plasmid: pSPL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q6NUD0 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.54 Å3/Da / Density % sol: 51.6 % / Mosaicity: 0.135 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 35%MPD, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.95→50 Å / Num. all: 49960 / Num. obs: 49895 / % possible obs: 99.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 6.3 % / Rmerge(I) obs: 0.15 / Χ2: 1.067 / Net I/σ(I): 5.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→37.898 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.794 / SU ML: 0.35 / σ(F): 1.42 / Phase error: 27.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 155.52 Å2 / Biso mean: 65.2201 Å2 / Biso min: 19.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.404 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→37.898 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: 14
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