+Open data
-Basic information
Entry | Database: PDB / ID: 1g4r | ||||||
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Title | CRYSTAL STRUCTURE OF BOVINE BETA-ARRESTIN 1 | ||||||
Components | BETA-ARRESTIN 1 | ||||||
Keywords | SIGNALING PROTEIN / Signal transduction / G-proteins / G-protein coupled receptors | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, SHARP / Resolution: 2.2 Å | ||||||
Authors | Schubert, C. / Han, M. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Crystal structure of beta-arrestin at 1.9 A: possible mechanism of receptor binding and membrane Translocation. Authors: Han, M. / Gurevich, V.V. / Vishnivetskiy, S.A. / Sigler, P.B. / Schubert, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g4r.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g4r.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 1g4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/1g4r ftp://data.pdbj.org/pub/pdb/validation_reports/g4/1g4r | HTTPS FTP |
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-Related structure data
Related structure data | 1g4mC 1cf1S 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: 44309.578 Da / Num. of mol.: 1 / Fragment: TRUNCATION MUTANT: 1-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PTRC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P17870 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.31 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 19 ℃ / pH: 8.5 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: May 24, 2000 / Details: mirrors and Si(111) |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→34 Å / Num. all: 29214 / Num. obs: 54018 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 4.6 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4041 / Rsym value: 50 / % possible all: 81.5 |
Reflection | *PLUS Num. obs: 27920 / % possible obs: 94.7 % / Redundancy: 9.6 % / Num. measured all: 267488 |
Reflection shell | *PLUS % possible obs: 79.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT, SHARP Starting model: 1CF1 Resolution: 2.2→32.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1571954.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.45 Å2 / ksol: 0.362 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→32.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor Rfree: 0.267 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 64.3 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.392 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.355 |