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Yorodumi- PDB-7zbe: Dark state crystal structure of bovine rhodopsin in Lipidic Cubic... -
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-Basic information
Entry | Database: PDB / ID: 7zbe | |||||||||
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Title | Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SwissFEL) | |||||||||
Components | Rhodopsin | |||||||||
Keywords | MEMBRANE PROTEIN / GPCR / Opsin / XFEL | |||||||||
Function / homology | Function and homology information Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / : ...Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / 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 / rhodopsin mediated 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 / detection of temperature stimulus involved in thermoception / outer membrane / arrestin family protein binding / photoreceptor cell maintenance / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor outer segment / G-protein alpha-subunit binding / sperm midpiece / visual perception / guanyl-nucleotide exchange factor activity / microtubule cytoskeleton organization / photoreceptor disc membrane / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / zinc ion binding / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Gruhl, T. / Weinert, T. / Rodrigues, M.J. / Milne, C. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P. / Cirelli, C. ...Gruhl, T. / Weinert, T. / Rodrigues, M.J. / Milne, C. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P. / 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. / Diethelm, A. / 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 | Switzerland, 2items
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Citation | Journal: Nature / Year: 2023 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: Journal: Biorxiv / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zbe.cif.gz | 334.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zbe.ent.gz | 225 KB | Display | PDB format |
PDBx/mmJSON format | 7zbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/7zbe ftp://data.pdbj.org/pub/pdb/validation_reports/zb/7zbe | HTTPS FTP |
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-Related structure data
Related structure data | 7zbcC 8a6cC 8a6dC 8a6eC 1u19S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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) Bos taurus (cattle) / References: UniProt: P02699 |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 6 types, 194 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density meas: 54.15 Mg/m3 / Density % sol: 54.6 % |
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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: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.38 Å |
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: 79305 / % possible obs: 100 % / Redundancy: 830.6 % / Biso Wilson estimate: 30.05 Å2 / CC1/2: 0.9926 / CC star: 0.9982 / R split: 0.0821 / Net I/σ(I): 7.62 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 556.7 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 7852 / CC1/2: 0.9926 / CC star: 0.8947 / R split: 1.0906 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U19 Resolution: 1.8→16.1 Å / SU ML: 0.2463 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.9592 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→16.1 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: -5.49013881869 Å / Origin y: 28.4181883411 Å / Origin z: 37.7945400539 Å
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Refinement TLS group | Selection details: all |