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Yorodumi- PDB-7mp2: CRYSTAL STRUCTURE OF NATIVE BOVINE ARRESTIN 1 IN COMPLEX WITH 1D-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mp2 | ||||||
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Title | CRYSTAL STRUCTURE OF NATIVE BOVINE ARRESTIN 1 IN COMPLEX WITH 1D-MYO-INOSITOL 1,5-BISDIPHOSPHATE TETRAKISPHOSPHATE (1,5-PP IP4) | ||||||
Components | S-arrestin | ||||||
Keywords | PROTEIN BINDING / GPCR / rhodopsin / phototransduction / inositol / 1 / 5PP-IP4 / IP8 | ||||||
Function / homology | Function and homology information opsin binding / Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / response to light stimulus / photoreceptor outer segment / photoreceptor inner segment / G protein-coupled receptor binding / phosphoprotein binding / signal transduction / membrane ...opsin binding / Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / response to light stimulus / photoreceptor outer segment / photoreceptor inner segment / G protein-coupled receptor binding / phosphoprotein binding / signal transduction / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å | ||||||
Authors | Sander, C.L. / Palczewski, K. / Kiser, P.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2022 Title: Structural evidence for visual arrestin priming via complexation of phosphoinositols. Authors: Sander, C.L. / Luu, J. / Kim, K. / Furkert, D. / Jang, K. / Reichenwallner, J. / Kang, M. / Lee, H.J. / Eger, B.T. / Choe, H.W. / Fiedler, D. / Ernst, O.P. / Kim, Y.J. / Palczewski, K. / Kiser, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mp2.cif.gz | 299.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mp2.ent.gz | 243.4 KB | Display | PDB format |
PDBx/mmJSON format | 7mp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/7mp2 ftp://data.pdbj.org/pub/pdb/validation_reports/mp/7mp2 | HTTPS FTP |
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-Related structure data
Related structure data | 7f1wC 7f1xC 7jsmC 7jtbSC 7jxaC 7morC 7mp0C 7mp1C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 45334.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P08168 #2: Chemical | ChemComp-I8P / ( #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: 3.94 Å3/Da / Density % sol: 68.76 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Bis-Tris propane, 35% 2-Ethoxyethanol, 0.001 mM Magnesium acetate, 5 mM 1D-MYO-INOSITOL 1,5-BISDIPHOSPHATE TETRAKISPHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 58102 / % possible obs: 99.7 % / Redundancy: 13.3 % / Biso Wilson estimate: 87.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.204 / Net I/σ(I): 12.71 |
Reflection shell | Resolution: 3→3.18 Å / Rmerge(I) obs: 3.623 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 9152 / CC1/2: 0.596 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 7JTB Resolution: 3→49.16 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 20.061 / SU ML: 0.316 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.852 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 288.38 Å2 / Biso mean: 104.153 Å2 / Biso min: 42.07 Å2
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Refinement step | Cycle: final / Resolution: 3→49.16 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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