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Yorodumi- PDB-5fa5: Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fa5 | ||||||
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Title | Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide | ||||||
Components |
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Keywords | TRANSFERASE/PROTEIN BINDING / Methyl Transferase / TRANSFERASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / histone H4R3 methyltransferase activity / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development ...positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / histone H4R3 methyltransferase activity / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone arginine N-methyltransferase activity / epithelial cell proliferation involved in prostate gland development / protein-arginine N-methyltransferase activity / methylosome / E-box binding / methyl-CpG binding / endothelial cell activation / histone H3 methyltransferase activity / positive regulation of mRNA splicing, via spliceosome / negative regulation of gene expression via chromosomal CpG island methylation / regulation of mitotic nuclear division / Cul4B-RING E3 ubiquitin ligase complex / histone methyltransferase complex / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway / arachidonate metabolic process / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / lipid oxidation / spliceosomal snRNP assembly / hepoxilin biosynthetic process / linoleic acid metabolic process / liver regeneration / nuclear receptor coactivator activity / regulation of signal transduction by p53 class mediator / methyltransferase activity / DNA-templated transcription termination / circadian regulation of gene expression / Regulation of TP53 Activity through Methylation / p53 binding / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / snRNP Assembly / ubiquitin-dependent protein catabolic process / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.34 Å | ||||||
Authors | Sprague, E.R. / McNamara, J.T. | ||||||
Citation | Journal: Science / Year: 2016 Title: Disordered methionine metabolism in MTAP/CDKN2A-deleted cancers leads to dependence on PRMT5. Authors: Mavrakis, K.J. / McDonald, E.R. / Schlabach, M.R. / Billy, E. / Hoffman, G.R. / deWeck, A. / Ruddy, D.A. / Venkatesan, K. / Yu, J. / McAllister, G. / Stump, M. / deBeaumont, R. / Ho, S. / ...Authors: Mavrakis, K.J. / McDonald, E.R. / Schlabach, M.R. / Billy, E. / Hoffman, G.R. / deWeck, A. / Ruddy, D.A. / Venkatesan, K. / Yu, J. / McAllister, G. / Stump, M. / deBeaumont, R. / Ho, S. / Yue, Y. / Liu, Y. / Yan-Neale, Y. / Yang, G. / Lin, F. / Yin, H. / Gao, H. / Kipp, D.R. / Zhao, S. / McNamara, J.T. / Sprague, E.R. / Zheng, B. / Lin, Y. / Cho, Y.S. / Gu, J. / Crawford, K. / Ciccone, D. / Vitari, A.C. / Lai, A. / Capka, V. / Hurov, K. / Porter, J.A. / Tallarico, J. / Mickanin, C. / Lees, E. / Pagliarini, R. / Keen, N. / Schmelzle, T. / Hofmann, F. / Stegmeier, F. / Sellers, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fa5.cif.gz | 384.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fa5.ent.gz | 313.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fa5_validation.pdf.gz | 737.7 KB | Display | wwPDB validaton report |
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Full document | 5fa5_full_validation.pdf.gz | 742.1 KB | Display | |
Data in XML | 5fa5_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 5fa5_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/5fa5 ftp://data.pdbj.org/pub/pdb/validation_reports/fa/5fa5 | HTTPS FTP |
-Related structure data
Related structure data | 4gqbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 74281.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 References: UniProt: O14744, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125 |
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#2: Protein | Mass: 39857.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR77, MEP50, WD45, HKMT1069, Nbla10071 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: Q9BQA1 |
#3: Protein/peptide | Mass: 2001.370 Da / Num. of mol.: 1 / Fragment: DNA binding residues 2-21 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805 |
#4: Chemical | ChemComp-MTA / |
#5: 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: 2.7 Å3/Da / Density % sol: 54.47 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop Details: 200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20) |
-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: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.34→89.22 Å / Num. obs: 53238 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 56.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Net I/σ(I): 17.2 / Num. measured all: 357014 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GQB Resolution: 2.34→89.22 Å / Cor.coef. Fo:Fc: 0.9334 / Cor.coef. Fo:Fc free: 0.9044 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.231 / SU Rfree Blow DPI: 0.191 / SU Rfree Cruickshank DPI: 0.195
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Displacement parameters | Biso max: 161.81 Å2 / Biso mean: 64.79 Å2 / Biso min: 29.52 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.34→89.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.34→2.4 Å / Total num. of bins used: 20
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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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