+Open data
-Basic information
Entry | Database: PDB / ID: 2i37 | |||||||||
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Title | Crystal structure of a photoactivated rhodopsin | |||||||||
Components | Rhodopsin | |||||||||
Keywords | MEMBRANE PROTEIN / trans-membrane protein / GPCR | |||||||||
Function / homology | Function and homology information Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly ...Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / 11-cis retinal binding / G protein-coupled photoreceptor activity / rod photoreceptor outer segment / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / response to light intensity / 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: 4.15 Å | |||||||||
Authors | Lodowski, D.T. / Stenkamp, R.E. / Salom, D. / Le Trong, I. / Palczewski, K. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Crystal structure of a photoactivated deprotonated intermediate of rhodopsin. Authors: Salom, D. / Lodowski, D.T. / Stenkamp, R.E. / Trong, I.L. / Golczak, M. / Jastrzebska, B. / Harris, T. / Ballesteros, J.A. / Palczewski, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i37.cif.gz | 180.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i37.ent.gz | 140.3 KB | Display | PDB format |
PDBx/mmJSON format | 2i37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i37_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2i37_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2i37_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 2i37_validation.cif.gz | 44.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/2i37 ftp://data.pdbj.org/pub/pdb/validation_reports/i3/2i37 | HTTPS FTP |
-Related structure data
Related structure data | 2i35C 2i36SC C: citing same article (ref.) 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ACE / Beg label comp-ID: ACE / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 1 / Auth seq-ID: 0 - 322 / Label seq-ID: 1 - 323
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-Components
#1: Protein | Mass: 39057.492 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02699 #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 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)-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 #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.59 Å3/Da / Density % sol: 73.21 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion / pH: 6.3 Details: 80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 0.1% sodium azide, 16 mM beta-mercaptoethanol, 2.6% Merpol HCS, equilibrated against 3.1-3.3 M ammonium sulfate, ...Details: 80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 0.1% sodium azide, 16 mM beta-mercaptoethanol, 2.6% Merpol HCS, equilibrated against 3.1-3.3 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9762 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 13, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 4.15→50 Å / Num. all: 12498 / Num. obs: 12498 / % possible obs: 76.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.063 / Χ2: 1.049 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 4.15→4.3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.86 / Num. unique all: 981 / Χ2: 0.833 / % possible all: 61.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2I36 Resolution: 4.15→30 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.867 / SU B: 133.351 / SU ML: 1.596 / Isotropic thermal model: single overall fixed B value / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 177.21 Å2
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Refinement step | Cycle: LAST / Resolution: 4.15→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 4586 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 4.15→4.26 Å / Total num. of bins used: 20
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