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Yorodumi- PDB-7z3j: Structure of crystallisable rat Phospholipase C gamma 1 in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z3j | ||||||
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Title | Structure of crystallisable rat Phospholipase C gamma 1 in complex with inositol 1,4,5-trisphosphate | ||||||
Components | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1 | ||||||
Keywords | HYDROLASE / HYDROLASE COMPLEX AUTOINHIBITED STATE | ||||||
Function / homology | Function and homology information PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / ISG15 antiviral mechanism / Generation of second messenger molecules ...PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / ISG15 antiviral mechanism / Generation of second messenger molecules / Phospholipase C-mediated cascade; FGFR2 / Downstream signal transduction / Signaling by ALK / Role of phospholipids in phagocytosis / inositol trisphosphate biosynthetic process / DAP12 signaling / FCERI mediated Ca+2 mobilization / VEGFR2 mediated cell proliferation / calcium-dependent phospholipase C activity / Synthesis of IP3 and IP4 in the cytosol / RET signaling / inositol trisphosphate metabolic process / response to curcumin / phosphoinositide phospholipase C / FCERI mediated MAPK activation / response to gravity / phosphatidylinositol metabolic process / phosphatidylinositol phospholipase C activity / COP9 signalosome / phospholipase C activity / neurotrophin TRKA receptor binding / positive regulation of endothelial cell apoptotic process / clathrin-coated vesicle / positive regulation of vascular endothelial cell proliferation / positive regulation of epithelial cell migration / phosphatidylinositol-mediated signaling / cellular response to epidermal growth factor stimulus / positive regulation of blood vessel endothelial cell migration / glutamate receptor binding / release of sequestered calcium ion into cytosol / ruffle / : / positive regulation of release of sequestered calcium ion into cytosol / guanyl-nucleotide exchange factor activity / epidermal growth factor receptor signaling pathway / cell projection / phosphoprotein binding / ruffle membrane / calcium-mediated signaling / insulin receptor binding / modulation of chemical synaptic transmission / response to hydrogen peroxide / Schaffer collateral - CA1 synapse / receptor tyrosine kinase binding / positive regulation of angiogenesis / calcium ion transport / cell-cell junction / cell migration / lamellipodium / T cell receptor signaling pathway / in utero embryonic development / glutamatergic synapse / calcium ion binding / protein kinase binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pinotsis, N. / Bunney, T.D. / Katan, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Characterization of the membrane interactions of phospholipase C gamma reveals key features of the active enzyme. Authors: Le Huray, K.I.P. / Bunney, T.D. / Pinotsis, N. / Kalli, A.C. / Katan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z3j.cif.gz | 562.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z3j.ent.gz | 379.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z3j_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7z3j_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7z3j_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 7z3j_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/7z3j ftp://data.pdbj.org/pub/pdb/validation_reports/z3/7z3j | HTTPS FTP |
-Related structure data
Related structure data | 6bpcS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 135990.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plcg1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P10686, phosphoinositide phospholipase C | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-I3P / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.91 % Description: ugly small crystals, however they diffract well |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 18.7 % PEG 3350, 0.1 M CBTP / PH range: 6.8-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 2→115.1 Å / Num. obs: 93254 / % possible obs: 98.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 49.37 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.076 / Net I/σ(I): 10.83 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 28825 / CC1/2: 0.234 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6bpc Resolution: 2→49.29 Å / SU ML: 0.3692 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.0714 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: 61.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→49.29 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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