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Yorodumi- PDB-4qj3: Structure of a fragment of human phospholipase C-beta3 delta472-5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qj3 | ||||||
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Title | Structure of a fragment of human phospholipase C-beta3 delta472-559, in complex with Galphaq | ||||||
Components |
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Keywords | SIGNALING PROTEIN/HYDROLASE / GTP-BINDING PROTEIN ALPHA SUBUNITS / PHOSPHOLIPASE C BETA / PH DOMAIN / EF HAND / C2 DOMAIN / TIM BARREL DOMAIN / GTP HYDROLYSIS / G-PROTEIN SIGNALING / LIPASE / CALCIUM BINDING / GTP BINDING / PHOSPHOLIPIDS / membrane / SIGNALING PROTEIN-HYDROLASE complex | ||||||
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 systemic arterial blood pressure / regulation of platelet activation / phosphatidylinositol phospholipase C activity / phospholipase C activity / maternal behavior / glutamate receptor signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / embryonic digit morphogenesis / postsynaptic cytosol / neuron remodeling / Synthesis of IP3 and IP4 in the cytosol / action potential / ligand-gated ion channel signaling pathway / negative regulation of potassium ion transport / phosphatidylinositol-mediated signaling / enzyme regulator activity / lipid catabolic process / release of sequestered calcium ion into cytosol / GTPase activator activity / positive regulation of smooth muscle cell proliferation / G protein activity / post-embryonic development / skeletal system development / molecular function activator activity / caveola / G protein-coupled receptor binding / regulation of blood pressure / G-protein beta/gamma-subunit complex binding / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / heterotrimeric G-protein complex / Ca2+ pathway / heart development / phospholipase C-activating G protein-coupled receptor signaling pathway / cell body / nuclear membrane / G alpha (q) signalling events / molecular adaptor activity / calmodulin binding / cadherin binding / G protein-coupled receptor signaling pathway / GTPase activity / synapse / dendrite / calcium ion binding / negative regulation of apoptotic process / protein-containing complex binding / GTP binding / 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: 3 Å | ||||||
Authors | Lyon, A.M. / Tesmer, J.J.G. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Molecular mechanisms of phospholipase C beta 3 autoinhibition. Authors: Lyon, A.M. / Begley, J.A. / Manett, T.D. / Tesmer, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qj3.cif.gz | 449.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qj3.ent.gz | 364.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qj3_validation.pdf.gz | 784.4 KB | Display | wwPDB validaton report |
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Full document | 4qj3_full_validation.pdf.gz | 786.8 KB | Display | |
Data in XML | 4qj3_validation.xml.gz | 36 KB | Display | |
Data in CIF | 4qj3_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/4qj3 ftp://data.pdbj.org/pub/pdb/validation_reports/qj/4qj3 | HTTPS FTP |
-Related structure data
Related structure data | 4qj4C 4qj5C 3ohm 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 44711.590 Da / Num. of mol.: 1 / Fragment: UNP residues 7-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnaq / Plasmid: pFastBac HTA / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P21279 |
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#2: Protein | Mass: 90294.156 Da / Num. of mol.: 1 / Fragment: UNP residues 10-891 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLCB3 / Plasmid: pFastBacDual / Production host: TRICHOPLUSIA NI (cabbage looper) References: UniProt: Q01970, phosphoinositide phospholipase C |
-Non-polymers , 5 types, 32 molecules
#3: Chemical | ChemComp-GDP / |
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#4: Chemical | ChemComp-ALF / |
#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-CA / |
#7: 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: 2.98 Å3/Da / Density % sol: 58.75 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM BisTris, 200 mM NaCl, 5% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2014 |
Radiation | Monochromator: KOHZU MONOCHROMATOR, CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. all: 31986 / Num. obs: 31965 / % possible obs: 99.8 % / Observed criterion σ(F): -2000 / Observed criterion σ(I): -2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.26 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.93 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OHM 3ohm Resolution: 3→29.71 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.898 / SU B: 38.029 / SU ML: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.394 / 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: 58.892 Å2
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Refinement step | Cycle: LAST / Resolution: 3→29.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.075 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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