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Yorodumi- PDB-7sq2: Reprocessed and refined structure of Phospholipase C-beta and Gq ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sq2 | ||||||||||||||||||
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Title | Reprocessed and refined structure of Phospholipase C-beta and Gq signaling complex | ||||||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / G-protein signaling Phopholipase-C Hydrolase Guanine nucleotide-binding protein G(q) alpha | ||||||||||||||||||
Function / homology | Function and homology information Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / phosphoinositide phospholipase C ...Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / phosphoinositide phospholipase C / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / G alpha (q) signalling events / Acetylcholine regulates insulin secretion / endothelin receptor signaling pathway / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / developmental pigmentation / phosphatidylinositol metabolic process / PLC beta mediated events / phospholipase C-activating dopamine receptor signaling pathway / cranial skeletal system development / ADP signalling through P2Y purinoceptor 1 / regulation of platelet activation / regulation of systemic arterial blood pressure / phosphatidylinositol phospholipase C activity / phospholipase C activity / maternal behavior / glutamate receptor signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / postsynaptic cytosol / action potential / neuron remodeling / embryonic digit morphogenesis / Synthesis of IP3 and IP4 in the cytosol / ligand-gated ion channel signaling pathway / negative regulation of potassium ion transport / phosphatidylinositol-mediated signaling / lipid catabolic process / enzyme regulator activity / release of sequestered calcium ion into cytosol / GTPase activator activity / post-embryonic development / G protein activity / skeletal system development / molecular function activator activity / caveola / G protein-coupled receptor binding / positive regulation of smooth muscle cell proliferation / G-protein beta/gamma-subunit complex binding / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / regulation of blood pressure / heterotrimeric G-protein complex / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / heart development / cell body / G alpha (q) signalling events / nuclear membrane / molecular adaptor activity / calmodulin binding / cadherin binding / G protein-coupled receptor signaling pathway / GTPase activity / synapse / calcium ion binding / dendrite / protein-containing complex binding / GTP binding / negative regulation of apoptotic process / Golgi apparatus / protein-containing complex / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||||||||
Authors | Endo-Streeter, S.T. / Sondek, J. / Harden, T.K. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Science / Year: 2010 Title: Kinetic Scaffolding Mediated by a Phospholipase C-{beta} and Gq Signaling Complex Authors: Endo-Streeter, S.T. / Sondek, J. / Harden, T.K. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sq2.cif.gz | 467.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sq2.ent.gz | 383 KB | Display | PDB format |
PDBx/mmJSON format | 7sq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sq2_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7sq2_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7sq2_validation.xml.gz | 42.5 KB | Display | |
Data in CIF | 7sq2_validation.cif.gz | 59.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/7sq2 ftp://data.pdbj.org/pub/pdb/validation_reports/sq/7sq2 | HTTPS FTP |
-Related structure data
Related structure data | 3ohm 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 38256.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnaq / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21279 |
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#2: Protein | Mass: 99865.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLCB3 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q01970, phosphoinositide phospholipase C |
-Non-polymers , 6 types, 227 molecules
#3: Chemical | ChemComp-ALF / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-GDP / | #6: Chemical | ChemComp-ACT / #7: Chemical | ChemComp-CA / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 3.04 Å3/Da / Density % sol: 59.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 7% PEG 6000, 100 mM Hepes, 1 mM CaCl2, 100 mM magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2010 / Details: Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: Si 220. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagittally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40.55 Å / Num. obs: 48454 / % possible obs: 99.49 % / Redundancy: 5.6 % / CC1/2: 0.905 / CC star: 0.975 / Rpim(I) all: 0.035 / Rrim(I) all: 0.084 / Χ2: 1.804 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 2.6→2.666 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.67 / Num. unique obs: 2555 / CC1/2: 0.905 / CC star: 0.975 / Rpim(I) all: 0.304 / Rrim(I) all: 0.723 / Χ2: 0.957 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OHM 3ohm Resolution: 2.6→40.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 29.23 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.444 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.472 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→40.55 Å
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Refine LS restraints |
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