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Yorodumi- PDB-2nym: Crystal Structure of Protein Phosphatase 2A (PP2A) with C-terminu... -
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-Basic information
Entry | Database: PDB / ID: 2nym | |||||||||
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Title | Crystal Structure of Protein Phosphatase 2A (PP2A) with C-terminus truncated catalytic subunit | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HEAT repeat / HYDROLASE-HYDROLASE INHIBITOR 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 / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / 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 / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / 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 / negative regulation of tyrosine phosphorylation of STAT protein / 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 / ceramide metabolic process / GABA receptor binding / negative regulation of epithelial to mesenchymal transition / 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 / regulation of Wnt signaling pathway / 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 / protein serine/threonine phosphatase activity / CTLA4 inhibitory signaling / Platelet sensitization by LDL / negative regulation of MAPK cascade / protein-serine/threonine phosphatase / regulation of cell differentiation / T cell homeostasis / ERK/MAPK targets / protein phosphatase activator activity / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / phosphoprotein phosphatase activity / mesoderm development / chromosome, centromeric region / DARPP-32 events / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of cell adhesion / Cyclin A/B1/B2 associated events during G2/M transition / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / 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 / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / protein dephosphorylation / RNA splicing / meiotic cell cycle / response to organic substance / protein tyrosine phosphatase activity / chromosome segregation / RHO GTPases Activate Formins / response to lead ion / regulation of protein phosphorylation / Spry regulation of FGF signaling / RAF activation / tau protein binding / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / positive regulation of protein serine/threonine kinase activity / negative regulation of cell growth / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / neuron projection Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Cyanobacteria (blue-green algae) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | |||||||||
Authors | Chen, Y. / Xing, Y. / Xu, Y. / Chao, Y. / Lin, Z. / Jeffrey, P.D. / Shi, Y. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: Structure of the Protein Phosphatase 2A Holoenzyme. Authors: Xu, Y. / Xing, Y. / Chen, Y. / Chao, Y. / Lin, Z. / Fan, E. / Yu, J.W. / Strack, S. / Jeffrey, P.D. / Shi, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nym.cif.gz | 517.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nym.ent.gz | 416.5 KB | Display | PDB format |
PDBx/mmJSON format | 2nym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/2nym ftp://data.pdbj.org/pub/pdb/validation_reports/ny/2nym | HTTPS FTP |
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-Related structure data
Related structure data | 2nppSC 2nylC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Each PP2A holoenzyme contains one scaffolding subunit, one catalytic subunit and one regulatory subunit |
-Components
#1: Protein | Mass: 65356.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96DH3, UniProt: P30153*PLUS #2: Protein | Mass: 46467.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5C, KIAA0044 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13362 #3: Protein | Mass: 33674.910 Da / Num. of mol.: 2 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 #4: Protein/peptide | #5: Chemical | ChemComp-MN / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10-15% PEG8000, 0.1 M Tris-Cl, 0.2 M magnesium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2006 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.6→100 Å / Num. all: 54875 / Num. obs: 53992 / % possible obs: 99.9 % / Rmerge(I) obs: 0.116 / Χ2: 1.025 / Net I/σ(I): 7.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NPP Resolution: 3.6→100 Å / σ(F): 0
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Solvent computation | Bsol: 72.069 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.175 Å2
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Refinement step | Cycle: LAST / Resolution: 3.6→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.6→3.73 Å | ||||||||||||||||||||||||||||
Xplor file |
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