+Open data
-Basic information
Entry | Database: PDB / ID: 4r7v | ||||||
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Title | Crystal structure of N-lobe of human ARRDC3(1-165) | ||||||
Components | Arrestin domain-containing protein 3 | ||||||
Keywords | PROTEIN BINDING / arrestin fold / GPCR down regulation / beta 2 adrenergic receptor | ||||||
Function / homology | Function and homology information negative regulation of heat generation / beta-3 adrenergic receptor binding / negative regulation of locomotion involved in locomotory behavior / positive regulation of hippo signaling / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of ubiquitin-protein transferase activity / heat generation / negative regulation of cold-induced thermogenesis / fat pad development / skin development ...negative regulation of heat generation / beta-3 adrenergic receptor binding / negative regulation of locomotion involved in locomotory behavior / positive regulation of hippo signaling / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of ubiquitin-protein transferase activity / heat generation / negative regulation of cold-induced thermogenesis / fat pad development / skin development / protein transport / lysosome / early endosome / endosome / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Qi, S. / Hurley, J. | ||||||
Citation | Journal: Protein Sci. / Year: 2014 Title: Insights into beta 2-adrenergic receptor binding from structures of the N-terminal lobe of ARRDC3. Authors: Qi, S. / O'Hayre, M. / Gutkind, J.S. / Hurley, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r7v.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r7v.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 4r7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/4r7v ftp://data.pdbj.org/pub/pdb/validation_reports/r7/4r7v | HTTPS FTP |
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-Related 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: 20017.283 Da / Num. of mol.: 1 / Fragment: UNP residues 1-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARRDC3, KIAA1376 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96B67 |
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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: 2.14 Å3/Da / Density % sol: 42.46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 0.1M Tris-HCl, 0.2M (NH4)2SO4, 50mM Guanidine-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2014 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→30 Å / Num. all: 17185 / Num. obs: 17177 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.73→1.79 Å / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→28.829 Å / SU ML: 0.15 / σ(F): 1.38 / Phase error: 23.73 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→28.829 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 23.5046 Å / Origin y: 22.8323 Å / Origin z: 16.3766 Å
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Refinement TLS group |
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