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Yorodumi- PDB-3dw8: Structure of a Protein Phosphatase 2A Holoenzyme with B55 subunit -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dw8 | |||||||||
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Title | Structure of a Protein Phosphatase 2A Holoenzyme with B55 subunit | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / holoenzyme / B55 / PR55 / WD repeat / Hydrolase / Iron / Manganese / Metal-binding / Methylation / Phosphoprotein / Protein phosphatase / 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 / 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 / negative regulation of epithelial to mesenchymal transition / 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 / response to morphine / 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 / 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 / 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 / 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 / meiotic cell cycle / 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 / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / 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 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 / nucleoplasm / membrane / metal ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Cyanobacteria (blue-green algae) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Xu, Y. / Chen, Y. / Zhang, P. / Jeffrey, P.D. / Shi, Y. | |||||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Structure of a protein phosphatase 2A holoenzyme: insights into B55-mediated Tau dephosphorylation. Authors: Xu, Y. / Chen, Y. / Zhang, P. / 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 | 3dw8.cif.gz | 524 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dw8.ent.gz | 419.7 KB | Display | PDB format |
PDBx/mmJSON format | 3dw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/3dw8 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/3dw8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 | The biological unit is a heterotrimer. There are two biological units in the asymmetric unit: first heterotrimer consisting of polypeptide chains A,B,C corresponding to PP2A subunits bound to catalytic MN atoms and MCLR inhibitor (chain G), and second heterotrimer consisting of polypeptide chains D,E,F corresponding to PP2A subunits bound to catalytic MN atoms and MCLR inhibitor (chain H). |
-Components
#1: Protein | Mass: 64762.785 Da / Num. of mol.: 2 / Fragment: A delta 8: Residues 9-589 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Production host: Escherichia coli (E. coli) / References: UniProt: P30153 #2: Protein | Mass: 51747.984 Da / Num. of mol.: 2 / Mutation: I310V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R2A / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63151 #3: Protein | Mass: 35636.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) 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: 3.11 Å3/Da / Density % sol: 60.47 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 7-10% PEG 35000, 0.10-0.15 M Sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→100 Å / Num. all: 87353 / Num. obs: 87353 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 65.9 Å2 |
Reflection shell | Resolution: 2.85→2.95 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PP2A A subunit, PP2A C subunit, WD40 ensemble Resolution: 2.85→49.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2550770.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.0084 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→49.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→3.03 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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