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Yorodumi- PDB-6zeg: Structure of PP1-IRSp53 chimera [PP1(7-304) + linker (G/S)x9 + IR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zeg | ||||||
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Title | Structure of PP1-IRSp53 chimera [PP1(7-304) + linker (G/S)x9 + IRSp53(449-465)] bound to Phactr1 (516-580) | ||||||
Components |
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Keywords | HYDROLASE / PP1 / Phosphatase / Phactr / RPEL | ||||||
Function / homology | Function and homology information neuron projection branch point / dendritic spine cytoplasm / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / dendrite arborization / plasma membrane organization / regulation of glycogen biosynthetic process / regulation of neuron migration / actin crosslink formation ...neuron projection branch point / dendritic spine cytoplasm / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / dendrite arborization / plasma membrane organization / regulation of glycogen biosynthetic process / regulation of neuron migration / actin crosslink formation / positive regulation of dendritic spine morphogenesis / cellular response to L-glutamate / protein localization to synapse / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / cytoskeletal anchor activity / regulation of modification of postsynaptic actin cytoskeleton / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / presynaptic cytosol / neuron projection terminus / actomyosin structure organization / regulation of canonical Wnt signaling pathway / proline-rich region binding / regulation of translational initiation / postsynaptic cytosol / protein phosphatase inhibitor activity / 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 / dendrite development / Triglyceride catabolism / Maturation of hRSV A proteins / entrainment of circadian clock by photoperiod / phosphatase activity / positive regulation of excitatory postsynaptic potential / phosphoprotein phosphatase activity / 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 / dephosphorylation / cellular response to epidermal growth factor stimulus / ruffle / RAC1 GTPase cycle / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / axonogenesis / dendritic shaft / synaptic membrane / secretory granule / filopodium / 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 / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / regulation of circadian rhythm / Regulation of actin dynamics for phagocytic cup formation / cerebral cortex development / VEGFA-VEGFR2 Pathway / Circadian Clock / presynapse / lamellipodium / insulin receptor signaling pathway / actin binding / regulation of cell shape / actin cytoskeleton organization / scaffold protein binding / perikaryon / microtubule / dendritic spine / cell cycle / cell division / neuronal cell body / glutamatergic synapse / synapse / nucleolus / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å | ||||||
Authors | Mouilleron, S. / Treisman, R. / Fedoryshchak, R. / Lee, R. / Butler, A.M. / Prechova, M. | ||||||
Citation | Journal: Elife / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zeg.cif.gz | 599 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zeg.ent.gz | 414.2 KB | Display | PDB format |
PDBx/mmJSON format | 6zeg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zeg_validation.pdf.gz | 751.4 KB | Display | wwPDB validaton report |
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Full document | 6zeg_full_validation.pdf.gz | 760 KB | Display | |
Data in XML | 6zeg_validation.xml.gz | 38.4 KB | Display | |
Data in CIF | 6zeg_validation.cif.gz | 58.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/6zeg ftp://data.pdbj.org/pub/pdb/validation_reports/ze/6zeg | HTTPS FTP |
-Related structure data
Related structure data | 6zeeC 6zefC 6zehC 6zeiC 6zejC 4movS 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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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 37678.723 Da / Num. of mol.: 2 / Mutation: N-terminal Vector derived sequence GHMGS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A, BAIAP2 / Production host: Escherichia coli (E. coli) 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.) Homo sapiens (human) / Gene: PHACTR1, hCG_1818446 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4VY12, UniProt: Q9C0D0*PLUS |
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-Non-polymers , 5 types, 854 molecules
#3: Chemical | ChemComp-MN / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-16P / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.32 Å3/Da / Density % sol: 47.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% (w/v) polyethylene glycol 3350, 0.2 M KSCN and 0.1 M BIS-Tris propane pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→37.18 Å / Num. obs: 332381 / % possible obs: 99.29 % / Redundancy: 2 % / Biso Wilson estimate: 10.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.018 / Rpim(I) all: 0.018 / Rrim(I) all: 0.026 / Net I/σ(I): 15.41 |
Reflection shell | Resolution: 1.09→1.13 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 62356 / CC1/2: 0.654 / Rpim(I) all: 0.44 / Rrim(I) all: 0.623 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MOV Resolution: 1.09→37.18 Å / SU ML: 0.0823 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.2494 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: 16.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.09→37.18 Å
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Refine LS restraints |
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LS refinement shell |
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