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Yorodumi- PDB-6k3f: Crystal Structure of beta-Arrestin 2 in Complex with CXCR7 Phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k3f | ||||||||||||
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Title | Crystal Structure of beta-Arrestin 2 in Complex with CXCR7 Phosphopeptide | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Complex | ||||||||||||
Function / homology | Function and homology information type 2A serotonin receptor binding / platelet activating factor receptor binding / postsynaptic signal transduction / positive regulation of synaptic transmission, dopaminergic / oculomotor nerve development / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / Activation of SMO / G alpha (s) signalling events / alpha-1B adrenergic receptor binding ...type 2A serotonin receptor binding / platelet activating factor receptor binding / postsynaptic signal transduction / positive regulation of synaptic transmission, dopaminergic / oculomotor nerve development / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / Activation of SMO / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / positive regulation of mesenchymal stem cell migration / angiotensin receptor binding / C-X-C chemokine binding / positive regulation of cardiac muscle cell differentiation / C-X-C chemokine receptor activity / WNT5A-dependent internalization of FZD4 / protein kinase B binding / MAP2K and MAPK activation / Ub-specific processing proteases / negative regulation of toll-like receptor signaling pathway / C-C chemokine receptor activity / Cargo recognition for clathrin-mediated endocytosis / C-C chemokine binding / Clathrin-mediated endocytosis / scavenger receptor activity / negative regulation of interleukin-12 production / regulation of G protein-coupled receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of calcium ion transport / arrestin family protein binding / G protein-coupled receptor internalization / type 1 angiotensin receptor binding / chemokine-mediated signaling pathway / adult walking behavior / Thrombin signalling through proteinase activated receptors (PARs) / Chemokine receptors bind chemokines / mitogen-activated protein kinase binding / positive regulation of epithelial cell apoptotic process / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of interleukin-1 beta production / positive regulation of DNA biosynthetic process / negative regulation of release of cytochrome c from mitochondria / detection of temperature stimulus involved in sensory perception of pain / negative regulation of smooth muscle cell apoptotic process / negative regulation of interleukin-6 production / positive regulation of receptor internalization / endocytic vesicle / negative regulation of tumor necrosis factor production / D1 dopamine receptor binding / positive regulation of collagen biosynthetic process / vasculogenesis / coreceptor activity / negative regulation of canonical NF-kappaB signal transduction / clathrin-coated pit / negative regulation of protein ubiquitination / cell chemotaxis / transforming growth factor beta receptor signaling pathway / 14-3-3 protein binding / negative regulation of protein phosphorylation / G protein-coupled receptor binding / calcium-mediated signaling / regulation of protein phosphorylation / modulation of chemical synaptic transmission / receptor internalization / recycling endosome / endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / protein transport / positive regulation of peptidyl-serine phosphorylation / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cytoplasmic vesicle / postsynaptic membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / angiogenesis / negative regulation of neuron apoptotic process / dendritic spine / transcription by RNA polymerase II / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / early endosome / cell adhesion / endosome / immune response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / intracellular membrane-bounded organelle / glutamatergic synapse / ubiquitin protein ligase binding / protein-containing complex binding / positive regulation of gene expression / enzyme binding Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Min, K.J. / Yoon, H.J. / Lee, H.H. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: Structure / Year: 2020 Title: Crystal Structure of beta-Arrestin 2 in Complex with CXCR7 Phosphopeptide. Authors: Min, K. / Yoon, H.J. / Park, J.Y. / Baidya, M. / Dwivedi-Agnihotri, H. / Maharana, J. / Chaturvedi, M. / Chung, K.Y. / Shukla, A.K. / Lee, H.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k3f.cif.gz | 782.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k3f.ent.gz | 650.4 KB | Display | PDB format |
PDBx/mmJSON format | 6k3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/6k3f ftp://data.pdbj.org/pub/pdb/validation_reports/k3/6k3f | HTTPS FTP |
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-Related structure data
Related structure data | 5w0pS 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: 42442.750 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arrb2 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P29067 #2: Protein/peptide | Mass: 1940.975 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P25106 #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.26 Å3/Da / Density % sol: 45.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium acetate, 0.1M Bis-Tris pH5.5, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.804 Å / Num. obs: 162425 / % possible obs: 99.67 % / Redundancy: 1 % / CC1/2: 0.711 / Net I/σ(I): 1.31 |
Reflection shell | Resolution: 1.95→2.07 Å / Num. unique obs: 49820 / CC1/2: 0.261 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W0P Resolution: 2.3→46.804 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.3 / Stereochemistry target values: TWIN_LSQ_F
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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: 89.25 Å2 / Biso mean: 25.3474 Å2 / Biso min: 13.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→46.804 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 50.6348 Å / Origin y: 63.5994 Å / Origin z: 51.391 Å
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Refinement TLS group |
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