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Yorodumi- PDB-4j4q: Crystal structure of active conformation of GPCR opsin stabilized... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j4q | |||||||||
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Title | Crystal structure of active conformation of GPCR opsin stabilized by octylglucoside | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / G-protein coupled receptor / Photoreceptor protein / Receptor Retinal protein / Transducer / Transmembrane / Glycoprotein / Lipoprotein / Sensory transduction / galpha subunit / GTP-binding / myristate / nucleotide-binding / Retinal Binding / Membrane | |||||||||
Function / homology | Function and homology information Opsins / VxPx cargo-targeting to cilium / rod bipolar cell differentiation / rod photoreceptor outer segment / sperm head plasma membrane / negative regulation of cyclic-nucleotide phosphodiesterase activity / podosome assembly / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) ...Opsins / VxPx cargo-targeting to cilium / rod bipolar cell differentiation / rod photoreceptor outer segment / sperm head plasma membrane / negative regulation of cyclic-nucleotide phosphodiesterase activity / podosome assembly / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / : / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / G protein-coupled opsin signaling pathway / 11-cis retinal binding / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / phototransduction, visible light / thermotaxis / Activation of the phototransduction cascade / outer membrane / detection of temperature stimulus involved in thermoception / arrestin family protein binding / photoreceptor cell maintenance / acyl binding / photoreceptor outer segment membrane / G alpha (i) signalling events / phototransduction / response to light stimulus / photoreceptor outer segment / G-protein alpha-subunit binding / sperm midpiece / photoreceptor inner segment / visual perception / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / microtubule cytoskeleton organization / photoreceptor disc membrane / GDP binding / heterotrimeric G-protein complex / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / GTPase activity / GTP binding / protein kinase binding / zinc ion binding / membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Park, J.H. / Morizumi, T. / Li, Y. / Hong, J.E. / Pai, E.F. / Hofmann, K.P. / Choe, H.W. / Ernst, O.P. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013 Title: Opsin, a structural model for olfactory receptors? Authors: Park, J.H. / Morizumi, T. / Li, Y. / Hong, J.E. / Pai, E.F. / Hofmann, K.P. / Choe, H.W. / Ernst, O.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j4q.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j4q.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 4j4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/4j4q ftp://data.pdbj.org/pub/pdb/validation_reports/j4/4j4q | HTTPS FTP |
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-Related structure data
Related structure data | 3dqbS 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 39031.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Strain: BovineBovinae / References: UniProt: P02699 |
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#2: Protein/peptide | Mass: 1261.487 Da / Num. of mol.: 1 / Fragment: C-terminal derived peptide, UNP RESIDUES 340-350 / Mutation: K341L, C347V / Source method: obtained synthetically Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED WITH K341L and C347V MUTATION Source: (synth.) Bos taurus (cattle) / References: UniProt: P04695 |
-Sugars , 3 types, 6 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose / |
#5: Sugar | ChemComp-BOG / |
-Non-polymers , 4 types, 36 molecules
#6: Chemical | ChemComp-PLM / | ||||
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#7: Chemical | #8: Chemical | ChemComp-ACT / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: AMMONIUM SULFATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL-DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→33.46 Å / Num. all: 35401 / Num. obs: 35401 / % possible obs: 99.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.421 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DQB Resolution: 2.65→33.46 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.824 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→33.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.718 Å / Total num. of bins used: 20
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