+Open data
-Basic information
Entry | Database: PDB / ID: 4iyp | ||||||
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Title | structure of the nPP2Ac-alpha4 complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / alpha4 / PP2A / latency / helix motif | ||||||
Function / homology | Function and homology information regulation of dephosphorylation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule-based movement / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / positive regulation of microtubule binding ...regulation of dephosphorylation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule-based movement / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / 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 / 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 / negative regulation of epithelial to mesenchymal transition / 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 stress-activated MAPK cascade / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / 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 / B cell activation / protein-serine/threonine phosphatase / regulation of cell differentiation / ERK/MAPK targets / T cell homeostasis / regulation of G1/S transition of mitotic cell cycle / phosphoprotein phosphatase activity / mesoderm development / chromosome, centromeric region / DARPP-32 events / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / response to tumor necrosis factor / 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 / Resolution of Sister Chromatid Cohesion / response to interleukin-1 / protein dephosphorylation / protein phosphatase 2A binding / meiotic cell cycle / protein tyrosine phosphatase activity / RHO GTPases Activate Formins / response to lead ion / regulation of protein phosphorylation / Spry regulation of FGF signaling / RAF activation / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / tau protein binding / 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 TP53 Degradation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / intracellular signal transduction / membrane raft / protein heterodimerization activity / synapse / negative regulation of transcription by RNA polymerase II / signal transduction / mitochondrion / extracellular exosome / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.797 Å | ||||||
Authors | Jiang, L. / Stanevich, V. / Satyshur, K.A. / Xing, Y. | ||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Structural basis of protein phosphatase 2A stable latency. Authors: Jiang, L. / Stanevich, V. / Satyshur, K.A. / Kong, M. / Watkins, G.R. / Wadzinski, B.E. / Sengupta, R. / Xing, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iyp.cif.gz | 147.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iyp.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 4iyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/4iyp ftp://data.pdbj.org/pub/pdb/validation_reports/iy/4iyp | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 25926.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: alpha4, IBP1, IGBP1 / Plasmid: pQlink / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P78318 |
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#2: Protein | Mass: 17896.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PP2Ac, ppp2c, PPP2CA / Plasmid: pQlink / Production host: Escherichia coli (E. coli) / Strain (production host): PP2A References: UniProt: P67775, protein-serine/threonine phosphatase |
#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: 3.61 Å3/Da / Density % sol: 65.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 12-15% PEG3350 (v/v), 0.3 M Na/K tartrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.797→50 Å / Num. all: 15948 / Num. obs: 15948 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.1 % / Rsym value: 0.07 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 2.797→2.85 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 3.22 / Num. unique all: 777 / Rsym value: 0.545 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.797→34.428 Å / SU ML: 0.33 / σ(F): 0.61 / Phase error: 22.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.797→34.428 Å
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Refine LS restraints |
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LS refinement shell |
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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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