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Yorodumi- PDB-1b3u: CRYSTAL STRUCTURE OF CONSTANT REGULATORY DOMAIN OF HUMAN PP2A, PR... -
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-Basic information
Entry | Database: PDB / ID: 1b3u | ||||||
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Title | CRYSTAL STRUCTURE OF CONSTANT REGULATORY DOMAIN OF HUMAN PP2A, PR65ALPHA | ||||||
Components | PROTEIN (PROTEIN PHOSPHATASE PP2A) | ||||||
Keywords | SCAFFOLD PROTEIN / PP2A / PHOSPHORYLATION / HEAT REPEAT | ||||||
Function / homology | Function and homology information meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / 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 / : / negative regulation of tyrosine phosphorylation of STAT protein ...meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / 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 / : / 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 / 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 / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of Wnt signaling pathway / regulation of growth / protein serine/threonine phosphatase activity / CTLA4 inhibitory signaling / Platelet sensitization by LDL / negative regulation of MAPK cascade / regulation of cell differentiation / T cell homeostasis / ERK/MAPK targets / regulation of DNA replication / chromosome, centromeric region / DARPP-32 events / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / 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 / 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 / response to organic substance / chromosome segregation / RHO GTPases Activate Formins / Spry regulation of FGF signaling / RAF activation / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / negative regulation of cell growth / 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 / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / neuron projection / protein heterodimerization activity / dendrite / neuronal cell body / glutamatergic synapse / apoptotic process / regulation of DNA-templated transcription / mitochondrion / extracellular exosome / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å | ||||||
Authors | Groves, M.R. / Hanlon, N. / Turowski, P. / Hemmings, B. / Barford, D. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: The structure of the protein phosphatase 2A PR65/A subunit reveals the conformation of its 15 tandemly repeated HEAT motifs. Authors: Groves, M.R. / Hanlon, N. / Turowski, P. / Hemmings, B.A. / Barford, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b3u.cif.gz | 246 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b3u.ent.gz | 199.4 KB | Display | PDB format |
PDBx/mmJSON format | 1b3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/1b3u ftp://data.pdbj.org/pub/pdb/validation_reports/b3/1b3u | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999932, -0.011239, 0.003138), Vector: |
-Components
#1: Protein | Mass: 65247.148 Da / Num. of mol.: 2 / Fragment: 65 KD REGULATORY SUBUNIT Source method: isolated from a genetically manipulated source Details: ALPHA ISOFORM / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28-M / Cell line (production host): B834 / Production host: Escherichia coli (E. coli) / References: UniProt: P30153 #2: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 64 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.3 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Aug 1, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 63661 / % possible obs: 82.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 7.2 / Rsym value: 0.097 / % possible all: 40.3 |
Reflection shell | *PLUS % possible obs: 40.3 % / Num. unique obs: 4473 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.3→25 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 1948906.6 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.85 Å2 / ksol: 0.309 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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