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Yorodumi- PDB-3uzs: Structure of the C13.28 RNA Aptamer Bound to the G Protein-Couple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uzs | ||||||
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Title | Structure of the C13.28 RNA Aptamer Bound to the G Protein-Coupled Receptor Kinase 2-Heterotrimeric G Protein Beta 1 and Gamma 2 Subunit Complex | ||||||
Components |
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Keywords | TRANSFERASE/RNA / Protein-RNA complex / Protein Kinase Fold / RGS Homology Domain / Pleckstrin Homology Domain / beta propeller / G Protein-Coupled Receptor Phosphorylation / RNA Aptamer / Carboxymethylation / geranylgeranylation / TRANSFERASE-RNA complex | ||||||
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 / Olfactory 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 / 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 / G protein-coupled receptor internalization / positive regulation of smoothened signaling pathway / 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 / 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 / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / presynapse / peptidyl-serine phosphorylation / postsynapse / protein kinase activity / G protein-coupled receptor signaling pathway / protein phosphorylation / GTPase activity / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.52 Å | ||||||
Authors | Tesmer, J.J.G. / Tesmer, V.M. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Molecular mechanism for inhibition of g protein-coupled receptor kinase 2 by a selective RNA aptamer. Authors: Tesmer, V.M. / Lennarz, S. / Mayer, G. / 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 | 3uzs.cif.gz | 466.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uzs.ent.gz | 380 KB | Display | PDB format |
PDBx/mmJSON format | 3uzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uzs_validation.pdf.gz | 481.1 KB | Display | wwPDB validaton report |
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Full document | 3uzs_full_validation.pdf.gz | 498.1 KB | Display | |
Data in XML | 3uzs_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 3uzs_validation.cif.gz | 52.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/3uzs ftp://data.pdbj.org/pub/pdb/validation_reports/uz/3uzs | HTTPS FTP |
-Related structure data
Related structure data | 3uztC 1omwS 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
#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: ADRBK1, GRK2 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P21146, beta-adrenergic-receptor kinase |
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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: Trichoplusia ni (cabbage looper) / 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: Trichoplusia ni (cabbage looper) / References: UniProt: P63212 |
#4: RNA chain | Mass: 9079.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic RNA polymer, no 5' or 3' phosphates |
#5: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.05 Å3/Da / Density % sol: 82.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris pH 8.5, 200 mM NaCl and 3% PEG 8000, 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-G / Wavelength: 0.97856 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 1, 2008 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→50 Å / Num. obs: 12758 / % possible obs: 58.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.064 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 4.5→4.58 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.388 / % possible all: 9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OMW Resolution: 4.52→19.99 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.919 / SU B: 178.994 / SU ML: 0.951 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 1.26 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 282.978 Å2
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Refinement step | Cycle: LAST / Resolution: 4.52→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.517→4.628 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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