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- PDB-6zei: Structure of PP1-IRSp53 S455E chimera [PP1(7-304) + linker (G/S)x... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zei | ||||||
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Title | Structure of PP1-IRSp53 S455E chimera [PP1(7-304) + linker (G/S)x9 + IRSp53(449-465)] bound to Phactr1 (516-580) | ||||||
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![]() | HYDROLASE / PP1 / Phosphatase / Phactr / RPEL | ||||||
Function / homology | ![]() neuron projection branch point / dendritic spine cytoplasm / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / dendrite arborization / regulation of glycogen biosynthetic process / plasma membrane organization / actin crosslink formation / regulation of neuron migration ...neuron projection branch point / dendritic spine cytoplasm / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / dendrite arborization / regulation of glycogen biosynthetic process / plasma membrane organization / actin crosslink formation / regulation of neuron migration / protein localization to synapse / cellular response to L-glutamate / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / cytoskeletal anchor activity / regulation of modification of postsynaptic actin cytoskeleton / positive regulation of dendritic spine morphogenesis / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / actomyosin structure organization / neuron projection terminus / presynaptic cytosol / proline-rich region binding / regulation of canonical Wnt signaling pathway / regulation of translational initiation / protein phosphatase inhibitor activity / postsynaptic cytosol / myosin phosphatase activity / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / positive regulation of actin filament polymerization / protein-serine/threonine phosphatase / stress fiber assembly / dephosphorylation / Triglyceride catabolism / dendrite development / Maturation of hRSV A proteins / entrainment of circadian clock by photoperiod / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / positive regulation of excitatory postsynaptic potential / actin filament bundle assembly / CDC42 GTPase cycle / excitatory synapse / DARPP-32 events / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / postsynaptic density, intracellular component / ribonucleoprotein complex binding / cellular response to epidermal growth factor stimulus / ruffle / RAC1 GTPase cycle / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / axonogenesis / secretory granule / filopodium / dendritic shaft / synaptic membrane / transcription coregulator binding / PDZ domain binding / cell motility / regulation of actin cytoskeleton organization / adherens junction / FCGR3A-mediated phagocytosis / response to lead ion / lung development / circadian regulation of gene expression / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / regulation of circadian rhythm / Regulation of actin dynamics for phagocytic cup formation / cerebral cortex development / VEGFA-VEGFR2 Pathway / Circadian Clock / insulin receptor signaling pathway / lamellipodium / presynapse / actin binding / regulation of cell shape / actin cytoskeleton organization / scaffold protein binding / perikaryon / microtubule / dendritic spine / cell division / neuronal cell body / glutamatergic synapse / synapse / nucleolus / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mouilleron, S. / Treisman, R. / Fedoryshchak, R. / Lee, R. / Butler, A.M. / Prechova, M. | ||||||
![]() | ![]() Title: Molecular basis for substrate specificity of the Phactr1/PP1 phosphatase holoenzyme. Authors: Fedoryshchak, R.O. / Prechova, M. / Butler, A. / Lee, R. / O'Reilly, N. / Flynn, H.R. / Snijders, A.P. / Eder, N. / Ultanir, S. / Mouilleron, S. / Treisman, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 571.9 KB | Display | ![]() |
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PDB format | ![]() | 395 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zeeC ![]() 6zefC ![]() 6zegC ![]() 6zehC ![]() 6zejC ![]() 4movS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 37720.758 Da / Num. of mol.: 2 / Mutation: N-terminal Vector derived sequence GHMGS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P62136, UniProt: Q9UQB8, protein-serine/threonine phosphatase #2: Protein | Mass: 8257.345 Da / Num. of mol.: 2 / Mutation: N-terminal Vector derived sequence GPLGS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 700 molecules ![](data/chem/img/MN.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
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![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MN / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 20% (w/v) polyethylene glycol 3350 and 0.2 M NaBr |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→69.37 Å / Num. obs: 162314 / % possible obs: 99.61 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Net I/σ(I): 12.54 |
Reflection shell | Resolution: 1.39→1.44 Å / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 15982 / CC1/2: 0.54 / Rpim(I) all: 0.52 / Rrim(I) all: 1.18 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MOV Resolution: 1.39→69.37 Å / SU ML: 0.1406 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.7329 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→69.37 Å
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Refine LS restraints |
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LS refinement shell |
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