+Open data
-Basic information
Entry | Database: PDB / ID: 5wkt | ||||||||||||
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Title | 3.2-Angstrom In situ Mylar structure of bovine opsin at 100 K | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / G protein-coupled receptor / GPCR / 7TM / ligand-free / in situ | ||||||||||||
Function / homology | Function and homology information Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly ...Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / 11-cis retinal binding / G protein-coupled photoreceptor activity / rod photoreceptor outer segment / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / response to light intensity / Activation of the phototransduction cascade / phototransduction, visible light / outer membrane / detection of temperature stimulus involved in thermoception / photoreceptor cell maintenance / arrestin family protein binding / photoreceptor outer segment membrane / G alpha (i) signalling events / phototransduction / photoreceptor outer segment / G-protein alpha-subunit binding / response to light stimulus / sperm midpiece / visual perception / guanyl-nucleotide exchange factor activity / photoreceptor disc membrane / microtubule cytoskeleton organization / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / zinc ion binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||||||||
Authors | Broecker, J. / Morizumi, T. / Ou, W.-L. / Ernst, O.P. | ||||||||||||
Funding support | Germany, Canada, United States, 3items
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Citation | Journal: Nat Protoc / Year: 2018 Title: High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions. Authors: Broecker, J. / Morizumi, T. / Ou, W.L. / Klingel, V. / Kuo, A. / Kissick, D.J. / Ishchenko, A. / Lee, M.Y. / Xu, S. / Makarov, O. / Cherezov, V. / Ogata, C.M. / 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 | 5wkt.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wkt.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 5wkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wkt_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5wkt_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5wkt_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 5wkt_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/5wkt ftp://data.pdbj.org/pub/pdb/validation_reports/wk/5wkt | HTTPS FTP |
-Related structure data
Related structure data | 5vraC 5wjkC 4j4qS 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
-Protein / Protein/peptide / Non-polymers , 3 types, 3 molecules AB
#1: Protein | Mass: 39031.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02699 |
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#2: Protein/peptide | Mass: 1261.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) |
#6: Chemical | ChemComp-SO4 / |
-Sugars , 3 types, 5 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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.74 Å3/Da / Density % sol: 84.11 % / Description: colorless, trigonal prismatic |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion / pH: 5.5 Details: 100 mM sodium acetate , 3.8 M (NH4)2SO4, ~12% (w/v) trehalose Temp details: 280-283 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→45.74 Å / Num. obs: 20539 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.97 / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J4Q Resolution: 3.2→45.74 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→45.74 Å
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Refine LS restraints |
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LS refinement shell |
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