[English] 日本語
Yorodumi- PDB-7juk: Crystal structure of PTEN with a tetra-phosphorylated tail (4p-cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7juk | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of PTEN with a tetra-phosphorylated tail (4p-crPTEN-13sp-T2, SDTTDSDPENEG) | ||||||||||||
Components | Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN | ||||||||||||
Keywords | SIGNALING PROTEIN / HYDROLASE / phosphatase / Phosphatidylinositol 3 / 4 / 5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase 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 / 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 / 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 / regulation of protein stability / cytoplasmic side of plasma membrane / PML body / Regulation of PTEN stability and activity / 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 / dendritic spine / postsynaptic density / learning or memory / protein stabilization / Ub-specific processing proteases / neuron projection / apical plasma membrane / negative regulation of cell population proliferation / lipid binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 Å | ||||||||||||
Model details | Crystal Structure of 4p-PTEN (aa 7-353+ 13 aa spacer, TGGGSGGTGGCRY+pSDpTpTDpSDPENEG | ||||||||||||
Authors | Dempsey, D. / Phan, K. / Cole, P. / Gabelli, S.B. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2021 Title: The structural basis of PTEN regulation by multi-site phosphorylation. Authors: Dempsey, D.R. / Viennet, T. / Iwase, R. / Park, E. / Henriquez, S. / Chen, Z. / Jeliazkov, J.R. / Palanski, B.A. / Phan, K.L. / Coote, P. / Gray, J.J. / Eck, M.J. / Gabelli, S.B. / Arthanari, H. / Cole, P.A. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7juk.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7juk.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 7juk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/7juk ftp://data.pdbj.org/pub/pdb/validation_reports/ju/7juk | HTTPS FTP |
---|
-Related structure data
Related structure data | 7jtxC 7julC 7jvxC 1d5rS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40886.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTEN, MMAC1, TEP1 / Plasmid: pfastbac / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P60484, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.34 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 1.2 M DL-malic acid |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Type: OTHER / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.15→80.217 Å / Num. all: 6346 / Num. obs: 6346 / % possible obs: 99.3 % / Redundancy: 6.6 % / Rpim(I) all: 0.059 / Rrim(I) all: 0.152 / Rsym value: 0.14 / Net I/av σ(I): 3.3 / Net I/σ(I): 8.8 / Num. measured all: 41598 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | ||||||
---|---|---|---|---|---|---|---|
Phasing MR | R rigid body: 0.39
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1D5R Resolution: 3.15→28.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.859 / WRfactor Rfree: 0.2907 / WRfactor Rwork: 0.183 / FOM work R set: 0.7737 / SU B: 28.893 / SU ML: 0.487 / SU Rfree: 0.6127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.613 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 219.49 Å2 / Biso mean: 90.408 Å2 / Biso min: 30 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.15→28.52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.15→3.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|