+Open data
-Basic information
Entry | Database: PDB / ID: 7df9 | ||||||
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Title | Crystal of Arrestin2-V2Rpp-1-Fab30 complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Arrestin / G-protein-coupled receptor / Phosphopeptide / Antibody fragment | ||||||
Function / homology | Function and homology information MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / clathrin heavy chain binding / Ub-specific processing proteases / clathrin coat of coated pit / desensitization of G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis ...MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / clathrin heavy chain binding / Ub-specific processing proteases / clathrin coat of coated pit / desensitization of G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / inositol hexakisphosphate binding / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / G protein-coupled receptor internalization / acetylcholine receptor binding / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / clathrin binding / negative regulation of Notch signaling pathway / small molecule binding / pseudopodium / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / visual perception / G protein-coupled receptor binding / receptor internalization / protein transport / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / signal transduction / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Mus musculus (house mouse) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å | ||||||
Authors | Sun, J.P. / Yu, X. / Xiao, P. / He, Q.T. / Lin, J.Y. / Zhu, Z.L. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural studies of phosphorylation-dependent interactions between the V2R receptor and arrestin-2. Authors: He, Q.T. / Xiao, P. / Huang, S.M. / Jia, Y.L. / Zhu, Z.L. / Lin, J.Y. / Yang, F. / Tao, X.N. / Zhao, R.J. / Gao, F.Y. / Niu, X.G. / Xiao, K.H. / Wang, J. / Jin, C. / Sun, J.P. / Yu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7df9.cif.gz | 166.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7df9.ent.gz | 122.8 KB | Display | PDB format |
PDBx/mmJSON format | 7df9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/7df9 ftp://data.pdbj.org/pub/pdb/validation_reports/df/7df9 | HTTPS FTP |
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-Related structure data
Related structure data | 7dfaC 7dfbC 7dfcC 4jqiS S: Starting model for refinement C: citing same article (ref.) |
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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: 48272.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ARRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P17870 |
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#2: Protein/peptide | Mass: 2996.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Antibody | Mass: 24751.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#4: Antibody | Mass: 26828.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / 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: 2.88 Å3/Da / Density % sol: 57.36 % |
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Crystal grow | Temperature: 289 K / Method: evaporation Details: 10% PEG 3350, 0.1M Succinic acid, pH 6.5-7.5, 0.2mM DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97736 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97736 Å / Relative weight: 1 |
Reflection | Resolution: 3.17→46.52 Å / Num. obs: 17687 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 101.63 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.17→3.39 Å / Rmerge(I) obs: 1.459 / Num. unique obs: 3145 / CC1/2: 0.783 / Rpim(I) all: 0.875 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4jqi Resolution: 3.17→38.25 Å / SU ML: 0.8259 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 37.9638 / Stereochemistry target values: CDL v1.2
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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 mean: 107.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.17→38.25 Å
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Refine LS restraints |
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LS refinement shell |
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