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Yorodumi- PDB-3uzt: Structure of the C13.18 RNA Aptamer in Complex with G Protein-Cou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uzt | ||||||
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Title | Structure of the C13.18 RNA Aptamer in Complex with G Protein-Coupled Receptor Kinase 2 | ||||||
Components |
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Keywords | TRANSFERASE/RNA / Protein-RNA complex / Protein Kinase Fold / RGS Homology Domain / Pleckstrin Homology Domain / G Protein-Coupled Receptor Phosphorylation / RNA Aptamer / 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 / 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 / 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 / positive regulation of smoothened signaling pathway / G protein-coupled receptor internalization / G alpha (s) signalling events / G alpha (q) signalling events / 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 / presynapse / heart development / postsynapse / peptidyl-serine phosphorylation / protein kinase activity / symbiont entry into host cell / G protein-coupled receptor signaling pathway / protein phosphorylation / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 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 | 3uzt.cif.gz | 267.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uzt.ent.gz | 215.3 KB | Display | PDB format |
PDBx/mmJSON format | 3uzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/3uzt ftp://data.pdbj.org/pub/pdb/validation_reports/uz/3uzt | HTTPS FTP |
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-Related structure data
Related structure data | 3uzsC 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: RNA chain | Mass: 5818.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic RNA polymer, no 5' or 3' phosphates |
#3: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 100 mM MES pH 5.9, 100 mM NaCl and 5% PEG 3350 supplemented with 0.1 M glycine, 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: Mar 18, 2010 |
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: 3.5→50 Å / Num. obs: 8251 / % possible obs: 65.5 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.7 / Num. unique all: 92 / % possible all: 14.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Chain A OF PDB ENTRY 1OMW Resolution: 3.51→24.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 107.159 / SU ML: 0.671 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -1.0E+18 / ESU R Free: 1.039 / 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: 129.331 Å2
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Refinement step | Cycle: LAST / Resolution: 3.51→24.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.51→3.597 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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