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Yorodumi- PDB-5swf: The structure of the PP2A B56 subunit double phosphorylated BubR1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5swf | |||||||||
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Title | The structure of the PP2A B56 subunit double phosphorylated BubR1 complex | |||||||||
Components |
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Keywords | Hydrolase / cell cycle / Phosphatase / Regulator / SLiM | |||||||||
Function / homology | Function and homology information mitotic checkpoint complex / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / metaphase/anaphase transition of mitotic cell cycle / protein phosphatase regulator activity / outer kinetochore / protein localization to chromosome, centromeric region ...mitotic checkpoint complex / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / metaphase/anaphase transition of mitotic cell cycle / protein phosphatase regulator activity / outer kinetochore / protein localization to chromosome, centromeric region / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / 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 / CTLA4 inhibitory signaling / Platelet sensitization by LDL / mitotic spindle assembly checkpoint signaling / protein phosphatase activator activity / chromosome, centromeric region / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / APC-Cdc20 mediated degradation of Nek2A / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RAF activation / Degradation of beta-catenin by the destruction complex / spindle / kinetochore / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Regulation of TP53 Degradation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / proteasome-mediated ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / cell division / negative regulation of cell population proliferation / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.818 Å | |||||||||
Authors | Page, R. / Wang, X. / Bajaj, R. / Peti, W. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Structure / Year: 2016 Title: Expanding the PP2A Interactome by Defining a B56-Specific SLiM. Authors: Wang, X. / Bajaj, R. / Bollen, M. / Peti, W. / Page, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5swf.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5swf.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 5swf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/5swf ftp://data.pdbj.org/pub/pdb/validation_reports/sw/5swf | HTTPS FTP |
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-Related structure data
Related structure data | 5k6sSC 5sw9C C: citing same article (ref.) S: Starting model for refinement |
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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: 41667.219 Da / Num. of mol.: 1 / Fragment: UNP residues 62-411 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5C, KIAA0044 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13362 |
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#2: Protein/peptide | Mass: 1162.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O60566*PLUS |
#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: 3.93 Å3/Da / Density % sol: 68.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.75 / Details: 8% PEG 8k, 0.8 M HEPES, 0.8 M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.818→39.511 Å / Num. obs: 16683 / % possible obs: 98.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.82→2.97 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.686 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5k6S Resolution: 2.818→39.5 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.818→39.5 Å
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Refine LS restraints |
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LS refinement shell |
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