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Yorodumi- PDB-2ie3: Structure of the Protein Phosphatase 2A Core Enzyme Bound to Tumo... -
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-Basic information
Entry | Database: PDB / ID: 2ie3 | |||||||||
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Title | Structure of the Protein Phosphatase 2A Core Enzyme Bound to Tumor-inducing Toxins | |||||||||
Components |
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Keywords | HYDROLASE/TOXIN / HEAT repeat / SIGNALING PROTEIN / HYDROLASE-TOXIN COMPLEX | |||||||||
Function / homology | Function and homology information meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / regulation of meiotic cell cycle process involved in oocyte maturation / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / peptidyl-serine dephosphorylation ...meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / regulation of meiotic cell cycle process involved in oocyte maturation / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / positive regulation of microtubule binding / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein antigen binding / protein phosphatase regulator activity / GABA receptor binding / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / ERKs are inactivated / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / negative regulation of epithelial to mesenchymal transition / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of growth / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / myosin phosphatase activity / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / Platelet sensitization by LDL / protein-serine/threonine phosphatase / regulation of cell differentiation / ERK/MAPK targets / T cell homeostasis / regulation of G1/S transition of mitotic cell cycle / mesoderm development / phosphoprotein phosphatase activity / chromosome, centromeric region / DARPP-32 events / lateral plasma membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / protein dephosphorylation / meiotic cell cycle / protein tyrosine phosphatase activity / chromosome segregation / RHO GTPases Activate Formins / response to lead ion / RAF activation / regulation of protein phosphorylation / Spry regulation of FGF signaling / Degradation of beta-catenin by the destruction complex / tau protein binding / PKR-mediated signaling / positive regulation of protein serine/threonine kinase activity / spindle pole / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Cyclin D associated events in G1 / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Degradation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / intracellular signal transduction / neuron projection / membrane raft / protein heterodimerization activity / neuronal cell body / glutamatergic synapse / synapse / dendrite / mitochondrion / extracellular exosome / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Cyanobacteria (blue-green algae) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Xing, Y. / Xu, Y. / Chen, Y. / Jeffrey, P.D. / Chao, Y. / Shi, Y. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: Structure of Protein Phosphatase 2A Core Enzyme Bound to Tumor-Inducing Toxins Authors: Xing, Y. / Xu, Y. / Chen, Y. / Jeffrey, P.D. / Chao, Y. / Lin, Z. / Li, Z. / Strack, S. / Stock, J.B. / Shi, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ie3.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ie3.ent.gz | 144.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ie3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ie3_validation.pdf.gz | 394.1 KB | Display | wwPDB validaton report |
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Full document | 2ie3_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 2ie3_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 2ie3_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/2ie3 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/2ie3 | HTTPS FTP |
-Related 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: 65378.344 Da / Num. of mol.: 1 / Fragment: scaffolding subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96DH3, UniProt: P30153*PLUS |
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#2: Protein | Mass: 35650.180 Da / Num. of mol.: 1 / Fragment: catalytic subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5 References: UniProt: P67775, protein-serine/threonine phosphatase |
#3: Protein/peptide | |
#4: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.49 Å3/Da / Density % sol: 72.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 mM lithium sulfate, 1.5 M ammonium sulfate, 0.1 M Tris-Cl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9796 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 44913 / Num. obs: 44149 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.061 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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