+Open data
-Basic information
Entry | Database: PDB / ID: 6fkb | ||||||
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Title | Crystal structure of N2C/D282C stabilized opsin bound to RS13 | ||||||
Components | Rhodopsin | ||||||
Keywords | MEMBRANE PROTEIN / RHODOPSIN / G PROTEIN-COUPLED RECEPTORS / RETINITIS PIGMENTOSA / SIGNALING PROTEIN / SENSORY TRANSDUCTION / PHOTORECEPTOR PROTEIN / KINTEGRAL MEMBRANE PROTEIN / VISION / MEMBRANE / RECEPTOR / TRANSDUCER PHOTORECEPTOR / SMALL MOLECULE COMPLEX | ||||||
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: 3.03 Å | ||||||
Authors | Mattle, D. / Standfuss, J. / Dawson, R. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Ligand channel in pharmacologically stabilized rhodopsin. Authors: Mattle, D. / Kuhn, B. / Aebi, J. / Bedoucha, M. / Kekilli, D. / Grozinger, N. / Alker, A. / Rudolph, M.G. / Schmid, G. / Schertler, G.F.X. / Hennig, M. / Standfuss, J. / Dawson, R.J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fkb.cif.gz | 151.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fkb.ent.gz | 121.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/6fkb ftp://data.pdbj.org/pub/pdb/validation_reports/fk/6fkb | HTTPS FTP |
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-Related structure data
Related structure data | 6fk6C 6fk7C 6fk8C 6fk9C 6fkaC 6fkcC 6fkdC 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 , 1 types, 1 molecules A
#1: Protein | Mass: 37057.574 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-326 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: RHO / Plasmid: PCMV-TET O / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: P02699 |
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-Sugars , 4 types, 10 molecules
#3: Sugar | #4: Sugar | ChemComp-BMA / | #5: Sugar | #6: Sugar | ChemComp-BOG / |
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-Non-polymers , 3 types, 4 molecules
#2: Chemical | ChemComp-PLM / |
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#7: Chemical | ChemComp-DLH / |
#8: 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: 8.11 Å3/Da |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: see publication |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.03→47.55 Å / Num. obs: 24484 / % possible obs: 99.9 % / Redundancy: 11.28 % / Rmerge(I) obs: 0.2624 / Rsym value: 0.2624 / Net I/σ(I): 6.89 |
Reflection shell | Resolution: 3.03→3.13 Å / Redundancy: 11.81 % / Rmerge(I) obs: 1.0302 / Mean I/σ(I) obs: 0.65 / Rsym value: 1.0302 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J4Q Resolution: 3.03→45.895 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.85 / 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: 3.03→45.895 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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