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Yorodumi- PDB-4o1v: SPOP Promotes Tumorigenesis by Acting as a Key Regulatory Hub in ... -
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-Basic information
Entry | Database: PDB / ID: 4o1v | ||||||
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Title | SPOP Promotes Tumorigenesis by Acting as a Key Regulatory Hub in Kidney Cancer | ||||||
Components |
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Keywords | PROTEIN BINDING / UBL conjugation pathway / ligase / ubiquitin / E3 / SPOP / MATH / PTEN | ||||||
Function / homology | Function and homology information inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of cellular component size / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity ...inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of cellular component size / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance / negative regulation of wound healing, spreading of epidermal cells / phosphatidylinositol-3-phosphate phosphatase activity / central nervous system neuron axonogenesis / postsynaptic density assembly / neuron-neuron synaptic transmission / negative regulation of dendritic spine morphogenesis / presynaptic membrane assembly / Regulation of PTEN mRNA translation / synapse maturation / Negative regulation of the PI3K/AKT network / cellular response to electrical stimulus / negative regulation of cell cycle G1/S phase transition / negative regulation of axonogenesis / Transcriptional Regulation by MECP2 / myelin sheath adaxonal region / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / negative regulation of excitatory postsynaptic potential / negative regulation of organ growth / forebrain morphogenesis / negative regulation of focal adhesion assembly / Schmidt-Lanterman incisure / negative regulation of epithelial to mesenchymal transition / phosphatidylinositol dephosphorylation / anaphase-promoting complex binding / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / dentate gyrus development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of proteolysis / positive regulation of ubiquitin protein ligase activity / positive regulation of ubiquitin-dependent protein catabolic process / spindle assembly involved in female meiosis / phosphatidylinositol biosynthetic process / dendritic spine morphogenesis / negative regulation of cell size / brain morphogenesis / myosin phosphatase activity / protein serine/threonine phosphatase activity / Cul3-RING ubiquitin ligase complex / negative regulation of G1/S transition of mitotic cell cycle / molecular function inhibitor activity / ubiquitin-specific protease binding / protein-serine/threonine phosphatase / regulation of neuron projection development / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of IP3 and IP4 in the cytosol / locomotor rhythm / negative regulation of vascular associated smooth muscle cell proliferation / social behavior / negative regulation of cellular senescence / phosphoprotein phosphatase activity / positive regulation of excitatory postsynaptic potential / Synthesis of PIPs at the plasma membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / canonical Wnt signaling pathway / multicellular organismal response to stress / localization / prepulse inhibition / negative regulation of peptidyl-serine phosphorylation / synapse assembly / Regulation of PTEN localization / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of cell migration / locomotory behavior / negative regulation of protein phosphorylation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / central nervous system development / protein tyrosine phosphatase activity / cell projection / PDZ domain binding / cell motility / TP53 Regulates Metabolic Genes / Hedgehog 'on' state / regulation of protein stability / cytoplasmic side of plasma membrane / PML body / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of DNA-binding transcription factor activity / cell migration / Ovarian tumor domain proteases / negative regulation of neuron projection development / Downstream TCR signaling / heart development / proteasome-mediated ubiquitin-dependent protein catabolic process / dendritic spine / postsynaptic density / learning or memory / protein stabilization Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Calabrese, M.F. / Watson, E.R. / Schulman, B.A. | ||||||
Citation | Journal: Cancer Cell / Year: 2014 Title: SPOP Promotes Tumorigenesis by Acting as a Key Regulatory Hub in Kidney Cancer. Authors: Li, G. / Ci, W. / Karmakar, S. / Chen, K. / Dhar, R. / Fan, Z. / Guo, Z. / Zhang, J. / Ke, Y. / Wang, L. / Zhuang, M. / Hu, S. / Li, X. / Zhou, L. / Li, X. / Calabrese, M.F. / Watson, E.R. / ...Authors: Li, G. / Ci, W. / Karmakar, S. / Chen, K. / Dhar, R. / Fan, Z. / Guo, Z. / Zhang, J. / Ke, Y. / Wang, L. / Zhuang, M. / Hu, S. / Li, X. / Zhou, L. / Li, X. / Calabrese, M.F. / Watson, E.R. / Prasad, S.M. / Rinker-Schaeffer, C. / Eggener, S.E. / Stricker, T. / Tian, Y. / Schulman, B.A. / Liu, J. / White, K.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o1v.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o1v.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 4o1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/4o1v ftp://data.pdbj.org/pub/pdb/validation_reports/o1/4o1v | HTTPS FTP |
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-Related structure data
Related structure data | 3ivvS S: Starting model for refinement |
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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: 16543.967 Da / Num. of mol.: 1 / Fragment: MATH domain (UNP residues 28-166) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: O43791 |
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#2: Protein/peptide | Mass: 1475.469 Da / Num. of mol.: 1 / Fragment: UNP residues 354-368 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P60484 |
#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: 38.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris, 100 mM sodium malonate, 36% PEG400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2011 |
Radiation | Monochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 9584 / % possible obs: 99.9 % / Redundancy: 3.7 % |
Reflection shell | Highest resolution: 2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IVV Resolution: 2→40.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.216 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40.99 Å
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Refine LS restraints |
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