+Open data
-Basic information
Entry | Database: PDB / ID: 6kl7 | ||||||||||||
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Title | Beta-arrestin 1 mutant S13D/T275D | ||||||||||||
Components | Beta-arrestin-1Arrestin | ||||||||||||
Keywords | SIGNALING PROTEIN / Beta-arrestin-1 / Signaling | ||||||||||||
Function / homology | Function and homology information V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / Activation of SMO / sensory perception of touch / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / angiotensin receptor binding ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / Activation of SMO / sensory perception of touch / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / angiotensin receptor binding / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / Golgi Associated Vesicle Biogenesis / MAP2K and MAPK activation / Ub-specific processing proteases / positive regulation of smooth muscle cell apoptotic process / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / regulation of G protein-coupled receptor signaling pathway / arrestin family protein binding / G protein-coupled receptor internalization / Thrombin signalling through proteinase activated receptors (PARs) / mitogen-activated protein kinase kinase binding / positive regulation of Rho protein signal transduction / clathrin binding / stress fiber assembly / negative regulation of Notch signaling pathway / pseudopodium / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of interleukin-6 production / positive regulation of receptor internalization / phototransduction / clathrin-coated pit / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / visual perception / GTPase activator activity / negative regulation of protein phosphorylation / positive regulation of protein ubiquitination / G protein-coupled receptor binding / nuclear estrogen receptor binding / phosphoprotein binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / endocytosis / protein transport / positive regulation of peptidyl-serine phosphorylation / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / postsynaptic membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / regulation of apoptotic process / negative regulation of neuron apoptotic process / transmembrane transporter binding / dendritic spine / positive regulation of MAPK cascade / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / protein ubiquitination / endosome / response to xenobiotic stimulus / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / signaling receptor binding / ubiquitin protein ligase binding / positive regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.794 Å | ||||||||||||
Authors | Kang, H. / Choi, H.J. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: Structure / Year: 2020 Title: Conformational Dynamics and Functional Implications of Phosphorylated beta-Arrestins. Authors: Kang, H. / Yang, H.S. / Ki, A.Y. / Ko, S.B. / Kim, K.W. / Shim, C.Y. / Kim, K. / Choi, H.J. / Chung, K.Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kl7.cif.gz | 296.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kl7.ent.gz | 239.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/6kl7 ftp://data.pdbj.org/pub/pdb/validation_reports/kl/6kl7 | HTTPS FTP |
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-Related structure data
Related structure data | 2wtrS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47543.977 Da / Num. of mol.: 2 / Mutation: S13D, T275D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arrb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29066 #2: Chemical | ChemComp-BA / #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.43 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.05 M HEPES 7.5, 70 mM BaCl2, 9% PEG 3550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.794→40 Å / Num. obs: 27394 / % possible obs: 98.68 % / Redundancy: 4 % / Biso Wilson estimate: 65.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07279 / Rpim(I) all: 0.04162 / Rrim(I) all: 0.0841 / Net I/σ(I): 12.89 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.5517 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2715 / CC1/2: 0.887 / Rpim(I) all: 0.3086 / Rrim(I) all: 0.6336 / % possible all: 98.15 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WTR Resolution: 2.794→39.096 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 224.09 Å2 / Biso mean: 95.914 Å2 / Biso min: 30.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.794→39.096 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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