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- PDB-8a6d: 10 picosecond light activated crystal structure of bovine rhodops... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8a6d | |||||||||
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Title | 10 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase | |||||||||
![]() | Rhodopsin | |||||||||
![]() | MEMBRANE PROTEIN / GPCR / Opsin | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Gruhl, T. / Weinert, T. / Rodrigues, M.J. / Milne, C.J. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P.J.M. / Cirelli, C. ...Gruhl, T. / Weinert, T. / Rodrigues, M.J. / Milne, C.J. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P.J.M. / Cirelli, C. / Furrer, A. / Mous, S. / Skopintsev, P. / James, D. / Dworkowski, F. / Baath, P. / Kekilli, D. / Oserov, D. / Tanaka, R. / Glover, H. / Bacellar, C. / Bruenle, S. / Casadei, C.M. / Diethelm, A.D. / Gashi, D. / Gotthard, G. / Guixa-Gonzalez, R. / Joti, Y. / Kabanova, V. / Knopp, G. / Lesca, E. / Ma, P. / Martiel, I. / Muehle, J. / Owada, S. / Pamula, F. / Sarabi, D. / Tejero, O. / Tsai, C.J. / Varma, N. / Wach, A. / Boutet, S. / Tono, K. / Nogly, P. / Deupi, X. / Iwata, S. / Neutze, R. / Standfuss, J. / Schertler, G.F.X. / Panneels, V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Ultrafast structural changes direct the first molecular events of vision. Authors: Gruhl, T. / Weinert, T. / Rodrigues, M.J. / Milne, C.J. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P.J.M. / Cirelli, C. / Furrer, A. / Mous, S. / Skopintsev, P. / James, D. / ...Authors: Gruhl, T. / Weinert, T. / Rodrigues, M.J. / Milne, C.J. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P.J.M. / Cirelli, C. / Furrer, A. / Mous, S. / Skopintsev, P. / James, D. / Dworkowski, F. / Bath, P. / Kekilli, D. / Ozerov, D. / Tanaka, R. / Glover, H. / Bacellar, C. / Brunle, S. / Casadei, C.M. / Diethelm, A.D. / Gashi, D. / Gotthard, G. / Guixa-Gonzalez, R. / Joti, Y. / Kabanova, V. / Knopp, G. / Lesca, E. / Ma, P. / Martiel, I. / Muhle, J. / Owada, S. / Pamula, F. / Sarabi, D. / Tejero, O. / Tsai, C.J. / Varma, N. / Wach, A. / Boutet, S. / Tono, K. / Nogly, P. / Deupi, X. / Iwata, S. / Neutze, R. / Standfuss, J. / Schertler, G. / Panneels, V. #1: ![]() Title: ULTRAFAST STRUCTURAL CHANGES DIRECT THE FIRST MOLECULAR EVENTS OF VISION Authors: Gruhl, T. / Weinert, T. / Rodrigues, M. / Milne, C.J. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P.J.M. / Cirelli, C. / Furrer, A. / Mous, S. / Skopintsev, P. / James, D. / ...Authors: Gruhl, T. / Weinert, T. / Rodrigues, M. / Milne, C.J. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P.J.M. / Cirelli, C. / Furrer, A. / Mous, S. / Skopintsev, P. / James, D. / Dworkowski, F. / Bath, P. / Kekilli, D. / Ozerov, D. / Tanaka, R. / Glover, H. / Bacellar, C. / Brunle, S. / Casadei, C.M. / Diethelm, A.D. / Gashi, D. / Gotthard, G. / Guixa-Gonzalez, R. / Joti, Y. / Kabanova, V. / Knopp, G. / Lesca, E. / Ma, P. / Martiel, I. / Muhle, J. / Owada, S. / Pamula, F. / Sarabi, D. / Tejero, O. / Tsai, C.J. / Varma, N. / Wach, A. / Boutet, S. / Tono, K. / Nogly, P. / Deupi, X. / Iwata, S. / Neutze, R. / Standfuss, J. / Schertler, G.F. / Panneels, V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 335 KB | Display | ![]() |
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PDB format | ![]() | 226.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 35.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zbcC ![]() 7zbeC ![]() 8a6cC ![]() 8a6eC ![]() 1u19S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39031.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 6 types, 134 molecules ![](data/chem/img/ACE.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/DAO.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/DAO.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #6: Chemical | ChemComp-DAO / | #7: Chemical | ChemComp-OLC / ( #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.15 % |
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Crystal grow | Temperature: 294 K / Method: lipidic cubic phase / pH: 9 / Details: 36 % PEG 600, 100 mM Bicine pH 9.0 |
-Data collection
Diffraction | Mean temperature: 294 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: PSI JUNGFRAU 1M / Detector: PIXEL / Date: Jul 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→16.1 Å / Num. obs: 79031 / % possible obs: 99.7 % / Redundancy: 595.9 % / Biso Wilson estimate: 30.44 Å2 / CC1/2: 0.9915 / CC star: 0.9979 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 0.72 / Num. unique obs: 79031 / CC1/2: 0.5081 / CC star: 0.8209 / R split: 1.3878 |
Serial crystallography sample delivery | Method: injection |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1U19 Resolution: 1.8→9.99 Å / SU ML: 0.4175 / Cross valid method: FREE R-VALUE / Phase error: 51.1655 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→9.99 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: -5.42370360115 Å / Origin y: 28.3745861112 Å / Origin z: 37.7684672506 Å
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Refinement TLS group | Selection details: all |