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Yorodumi- PDB-1omw: Crystal Structure of the complex between G Protein-Coupled Recept... -
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-Basic information
Entry | Database: PDB / ID: 1omw | ||||||
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Title | Crystal Structure of the complex between G Protein-Coupled Receptor Kinase 2 and Heterotrimeric G Protein beta 1 and gamma 2 subunits | ||||||
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Keywords | TRANSFERASE / WD-40 repeat | ||||||
Function / homology | Function and homology information Calmodulin induced events / beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / Activation of SMO / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / tachykinin receptor signaling pathway ...Calmodulin induced events / beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / Activation of SMO / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / tachykinin receptor signaling pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / negative regulation of striated muscle contraction / desensitization of G protein-coupled receptor signaling pathway / positive regulation of protein localization to cilium / Cargo recognition for clathrin-mediated endocytosis / regulation of the force of heart contraction / Activation of the phototransduction cascade / positive regulation of smoothened signaling pathway / G protein-coupled receptor internalization / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / regulation of signal transduction / cardiac muscle contraction / viral genome replication / cell projection / G protein-coupled receptor binding / intracellular protein transport / G protein-coupled acetylcholine receptor signaling pathway / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / sensory perception of taste / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / presynapse / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / heart development / postsynapse / peptidyl-serine phosphorylation / cell population proliferation / protein kinase activity / symbiont entry into host cell / G protein-coupled receptor signaling pathway / protein phosphorylation / GTPase activity / protein-containing complex binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Lodowski, D.T. / Pitcher, J.A. / Capel, W.D. / Lefkowitz, R.J. / Tesmer, J.J.G. | ||||||
Citation | Journal: Science / Year: 2003 Title: Keeping G proteins at Bay: A Complex Between G Protein-Coupled Receptor Kinase 2 and G-Beta-Gamma Authors: Lodowski, D.T. / Pitcher, J.A. / Capel, W.D. / Lefkowitz, R.J. / Tesmer, J.J.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1omw.cif.gz | 213.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1omw.ent.gz | 169.6 KB | Display | PDB format |
PDBx/mmJSON format | 1omw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/1omw ftp://data.pdbj.org/pub/pdb/validation_reports/om/1omw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 79749.922 Da / Num. of mol.: 1 / Mutation: S670A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P21146, EC: 2.7.1.126 |
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#2: Protein | Mass: 37416.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P62871 |
#3: Protein | Mass: 8406.658 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P63212 |
#4: 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: 3 Å3/Da / Density % sol: 59.3 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: PEG 3350, Sodium Chloride, CHAPS, ATP, Magnesium Chloride, Mastoparan , MES pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Lodowski, D.T., (2003) Acta Crystallogr., D59, 936. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.5→20 Å / Num. all: 135084 / Num. obs: 56160 / % possible obs: 73.6 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 2.4 % / Biso Wilson estimate: 37.42 Å2 / Rsym value: 0.05 / Net I/σ(I): 15.3 | ||||||||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 0.67 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1977 / Rsym value: 0.253 / % possible all: 12.7 | ||||||||||||||||||
Reflection | *PLUS Num. obs: 38258 / Rmerge(I) obs: 0.053 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 12.7 % / Rmerge(I) obs: 0.253 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ABG, 1ATP, 1BAK, 1DK8 Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.95 / SU B: 10.266 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement Cross valid method: The structure was initally solved with R-free as the cross validation method, but for the last three rounds of refinement, the structure was refined against all of the data. σ(F): -2 / ESU R: 0.72 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the extreme anisotropy of the data, a three dimensional ellipsoid with resolution limits corresponding to the maximum diffraction in ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the extreme anisotropy of the data, a three dimensional ellipsoid with resolution limits corresponding to the maximum diffraction in each direction was defined to select reflections used in refinement. These diffraction limits were 2.4, 2.8, 3.0 Angstroms. The 2.4 A direction corresponds to 37.9 degrees inclined from the a* axis, the 2.8 A direction corresponds to the b* axis and the 3.0 A direction corresponds to direction 1 X b*.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.933 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 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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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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