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Open data
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Basic information
Entry | Database: PDB / ID: 6fk8 | |||||||||
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Title | Crystal structure of N2C/D282C stabilized opsin bound to RS08 | |||||||||
![]() | Rhodopsin | |||||||||
![]() | 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 | ![]() Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / rod photoreceptor outer segment / sperm head plasma membrane / absorption of visible light / The canonical retinoid cycle in rods (twilight vision) / : / photoreceptor inner segment membrane ...Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / rod photoreceptor outer segment / sperm head plasma membrane / absorption of visible light / The canonical retinoid cycle in rods (twilight vision) / : / photoreceptor inner segment membrane / podosome assembly / G protein-coupled opsin signaling pathway / 11-cis retinal binding / G protein-coupled photoreceptor activity / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mattle, D. / Standfuss, J. / Dawson, R. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156 KB | Display | ![]() |
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PDB format | ![]() | 122.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fk6C ![]() 6fk7C ![]() 6fk9C ![]() 6fkaC ![]() 6fkbC ![]() 6fkcC ![]() 6fkdC ![]() 4j4qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 39034.586 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-326 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 |
#3: Chemical | ChemComp-PLM / |
#4: Chemical | ChemComp-DNZ / ( |
#5: Sugar |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 8.03 Å3/Da / Density % sol: 84.22 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→45.77 Å / Num. obs: 28482 / % possible obs: 100 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.1926 / Rsym value: 0.1926 / Net I/σ(I): 12.28 |
Reflection shell | Resolution: 2.87→2.97 Å / Redundancy: 11.5 % / Rmerge(I) obs: 3.531 / Mean I/σ(I) obs: 0.72 / Rsym value: 3.531 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4J4Q Resolution: 2.87→45.77 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.41 / 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: 2.87→45.77 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: 27.9754 Å / Origin y: 389.1563 Å / Origin z: 39.0769 Å
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Refinement TLS group | Selection details: all |