+Open data
-Basic information
Entry | Database: PDB / ID: 2ped | |||||||||
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Title | Crystallographic model of 9-cis-rhodopsin | |||||||||
Components | Rhodopsin | |||||||||
Keywords | SIGNALING PROTEIN / RHODOPSIN / G PROTEIN-COUPLED RECEPTOR / VISUAL PIGMENT | |||||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | |||||||||
Authors | Nakamichi, H. / Okada, T. | |||||||||
Citation | Journal: Biophys.J. / Year: 2007 Title: Photoisomerization mechanism of rhodopsin and 9-cis-rhodopsin revealed by x-ray crystallography Authors: Nakamichi, H. / Buss, V. / Okada, T. #1: Journal: J.Am.Chem.Soc. / Year: 2007 Title: Protein assistance in the photoisomerization of rhodopsin and 9-cis-rhodopsin--insights from experiment and theory Authors: Sekharan, S. / Sugihara, M. / Weingart, O. / Okada, T. / Buss, V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ped.cif.gz | 163.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ped.ent.gz | 128.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ped.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ped_validation.pdf.gz | 981.7 KB | Display | wwPDB validaton report |
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Full document | 2ped_full_validation.pdf.gz | 1008.1 KB | Display | |
Data in XML | 2ped_validation.xml.gz | 25 KB | Display | |
Data in CIF | 2ped_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/2ped ftp://data.pdbj.org/pub/pdb/validation_reports/pe/2ped | HTTPS FTP |
-Related structure data
Related structure data | 1u19S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) Bos taurus (cattle) / References: UniProt: P02699 |
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-Sugars , 4 types, 8 molecules
#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, 130 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.44 Å3/Da / Density % sol: 72.32 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.9M AMMONIUM SULFATE, 0.05M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 25, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 27964 / % possible obs: 91.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 8.27 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1.06 / Num. unique all: 1615 / % possible all: 53.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U19 Resolution: 2.95→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 76.849 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.95→50 Å
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Refine LS restraints |
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