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Yorodumi- PDB-4ekd: Structure of human regulator of G protein signaling 2 (RGS2) in c... -
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-Basic information
Entry | Database: PDB / ID: 4ekd | ||||||
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Title | Structure of human regulator of G protein signaling 2 (RGS2) in complex with murine Galpha-q(R183C) | ||||||
Components |
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Keywords | SIGNALING PROTEIN/INHIBITOR / GTP-binding / Regulator of G protein signaling / homology domain / GTPase activation / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway / negative regulation of phospholipase activity / negative regulation of glycine import across plasma membrane / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / adenylate cyclase inhibitor activity / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding ...regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway / negative regulation of phospholipase activity / negative regulation of glycine import across plasma membrane / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / adenylate cyclase inhibitor activity / 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 / G alpha (q) signalling events / 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 / negative regulation of cardiac muscle hypertrophy / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of G protein-coupled receptor signaling pathway / phospholipase C-activating dopamine receptor signaling pathway / cranial skeletal system development / regulation of platelet activation / ADP signalling through P2Y purinoceptor 1 / maternal behavior / regulation of G protein-coupled receptor signaling pathway / relaxation of vascular associated smooth muscle / glutamate receptor signaling pathway / regulation of canonical Wnt signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / relaxation of cardiac muscle / action potential / neuron remodeling / embryonic digit morphogenesis / beta-tubulin binding / ligand-gated ion channel signaling pathway / negative regulation of potassium ion transport / G-protein alpha-subunit binding / maternal process involved in female pregnancy / enzyme regulator activity / brown fat cell differentiation / positive regulation of cardiac muscle contraction / response to amphetamine / GTPase activator activity / post-embryonic development / negative regulation of MAP kinase activity / G protein activity / skeletal system development / G protein-coupled receptor binding / caveola / positive regulation of smooth muscle cell proliferation / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cytoplasmic side of plasma membrane / positive regulation of neuron projection development / positive regulation of insulin secretion / regulation of blood pressure / heterotrimeric G-protein complex / cell body / phospholipase C-activating G protein-coupled receptor signaling pathway / heart development / G alpha (q) signalling events / spermatogenesis / response to ethanol / nuclear membrane / negative regulation of translation / protein stabilization / calmodulin binding / cell cycle / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / synapse / protein-containing complex binding / GTP binding / nucleolus / negative regulation of apoptotic process / Golgi apparatus / mitochondrion / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Tesmer, J.J.G. / Nance, M.R. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structural and functional analysis of the regulator of G protein signaling 2-g alpha q complex. Authors: Nance, M.R. / Kreutz, B. / Tesmer, V.M. / Sterne-Marr, R. / Kozasa, T. / 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 | 4ekd.cif.gz | 206.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ekd.ent.gz | 165.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ekd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/4ekd ftp://data.pdbj.org/pub/pdb/validation_reports/ek/4ekd | HTTPS FTP |
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-Related structure data
Related structure data | 4ekcC 2af0S 2bcjS 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 40634.172 Da / Num. of mol.: 1 / Fragment: UNP residues 18-359 / Mutation: E125D, N126V, Y128D, V129Y, D130A, R183C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnaq / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P21279, EC: 3.6.5.1 |
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#2: Protein | Mass: 15871.833 Da / Num. of mol.: 1 / Fragment: RGS domain, UNP residues 72-203 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RGS2, G0S8, GIG31 / Production host: Escherichia coli (E. coli) / References: UniProt: P41220 |
-Non-polymers , 7 types, 24 molecules
#3: Chemical | ChemComp-GDP / | ||||||||
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#4: Chemical | ChemComp-ALF / | ||||||||
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MG / | #8: Chemical | ChemComp-MES / | #9: 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: 2.77 Å3/Da / Density % sol: 55.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 12% PEG 8,000, 15 mM CoCl2, 200 mM NaCl, and 100 mM MES 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 13, 2010 / Details: KB Bimorph Mirrors |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0782 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 12037 / Num. obs: 11782 / % possible obs: 64 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.065 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 189 / Rsym value: 0.441 / % possible all: 21.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2AF0 and 2BCJ Resolution: 2.71→29.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 44.27 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / 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: 96.352 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→29.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.782 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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