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Yorodumi- PDB-8as2: Structure of arrestin2 in complex with 4P CCR5 phosphopeptide and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8as2 | ||||||
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Title | Structure of arrestin2 in complex with 4P CCR5 phosphopeptide and Fab30 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / arrestin / GPCR | ||||||
Function / homology | Function and homology information angiotensin receptor binding / Activation of SMO / negative regulation of interleukin-8 production / arrestin family protein binding / G protein-coupled receptor internalization / enzyme inhibitor activity / Lysosome Vesicle Biogenesis / positive regulation of Rho protein signal transduction / negative regulation of NF-kappaB transcription factor activity / Golgi Associated Vesicle Biogenesis ...angiotensin receptor binding / Activation of SMO / negative regulation of interleukin-8 production / arrestin family protein binding / G protein-coupled receptor internalization / enzyme inhibitor activity / Lysosome Vesicle Biogenesis / positive regulation of Rho protein signal transduction / negative regulation of NF-kappaB transcription factor activity / Golgi Associated Vesicle Biogenesis / negative regulation of Notch signaling pathway / stress fiber assembly / pseudopodium / negative regulation of interleukin-6 production / positive regulation of receptor internalization / clathrin-coated pit / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / visual perception / Activated NOTCH1 Transmits Signal to the Nucleus / GTPase activator activity / G protein-coupled receptor binding / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cytoplasmic vesicle membrane / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / protein transport / Thrombin signalling through proteinase activated receptors (PARs) / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / nuclear body / Ub-specific processing proteases / protein ubiquitination / positive regulation of protein phosphorylation / Golgi membrane / lysosomal membrane / ubiquitin protein ligase binding / chromatin / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Phage display vector pTDisp (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Isaikina, P. / Jakob, R.P. / Maier, T. / Grzesiek, S. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Mol.Cell / Year: 2023 Title: A key GPCR phosphorylation motif discovered in arrestin2⋅CCR5 phosphopeptide complexes. Authors: Isaikina, P. / Petrovic, I. / Jakob, R.P. / Sarma, P. / Ranjan, A. / Baruah, M. / Panwalkar, V. / Maier, T. / Shukla, A.K. / Grzesiek, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8as2.cif.gz | 332.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8as2.ent.gz | 271.8 KB | Display | PDB format |
PDBx/mmJSON format | 8as2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/8as2 ftp://data.pdbj.org/pub/pdb/validation_reports/as/8as2 | HTTPS FTP |
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-Related structure data
Related structure data | 8as3C 8as4C 4jqiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40319.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARRB1, ARR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49407 |
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#2: Protein/peptide | Mass: 2659.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: Antibody | Mass: 25053.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phage display vector pTDisp (others) / Production host: Escherichia coli (E. coli) |
#4: Antibody | Mass: 23992.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phage display vector pTDisp (others) / Production host: Escherichia coli (E. coli) |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1% tryptone (w/v), 0.05M HEPES, 12 % PEG3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→49.49 Å / Num. obs: 17440 / % possible obs: 98.8 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.313 / Rpim(I) all: 0.128 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 7 % / Rmerge(I) obs: 1.866 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1676 / CC1/2: 0.673 / Rpim(I) all: 0.761 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4jqi Resolution: 3.2→49.49 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.26 / 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: 519.22 Å2 / Biso mean: 197.406 Å2 / Biso min: 98.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→49.49 Å
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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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