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- PDB-1u19: Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 1u19 | |||||||||
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Title | Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution | |||||||||
![]() | Rhodopsin | |||||||||
![]() | SIGNALING PROTEIN / G PROTEIN-COUPLED RECEPTOR / MEMBRANE PROTEIN / RETINAL PROTEIN / PHOTORECEPTOR | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Okada, T. / Sugihara, M. / Bondar, A.N. / Elstner, M. / Entel, P. / Buss, V. | |||||||||
![]() | ![]() Title: The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure Authors: Okada, T. / Sugihara, M. / Bondar, A.N. / Elstner, M. / Entel, P. / Buss, 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 | ![]() | 162.8 KB | Display | ![]() |
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PDB format | ![]() | 127.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 950.2 KB | Display | ![]() |
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Full document | ![]() | 1013.7 KB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 35.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1l9hS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39057.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 4 types, 8 molecules ![](data/chem/img/HTG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-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 #9: Sugar | ChemComp-HTG / |
-Non-polymers , 6 types, 88 molecules ![](data/chem/img/HG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-HG / #6: Chemical | ChemComp-ZN / #7: Chemical | #8: Chemical | ChemComp-PLM / #10: Chemical | ChemComp-HTO / | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 71 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 198898 / Num. obs: 61728 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 1.2 / % possible all: 46.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L9H Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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