[English] 日本語
Yorodumi- PDB-2x72: CRYSTAL STRUCTURE OF THE CONSTITUTIVELY ACTIVE E113Q,D2C,D282C RH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x72 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE CONSTITUTIVELY ACTIVE E113Q,D2C,D282C RHODOPSIN MUTANT WITH BOUND GALPHACT PEPTIDE. | |||||||||
Components |
| |||||||||
Keywords | SIGNALING PROTEIN / CHROMOPHORE / LIPOPROTEIN / GLYCOPROTEIN / TRANSMEMBRANE / RETINAL PROTEIN / G-PROTEIN COUPLED RECEPTOR / SENSORY TRANSDUCTION / PHOTORECEPTOR PROTEIN | |||||||||
Function / homology | Function and homology information Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / negative regulation of cyclic-nucleotide phosphodiesterase activity / 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 / negative regulation of cyclic-nucleotide phosphodiesterase activity / 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 / acyl binding / 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 / photoreceptor inner segment / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / microtubule cytoskeleton organization / photoreceptor disc membrane / GDP binding / heterotrimeric G-protein complex / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / GTPase activity / GTP binding / protein kinase binding / zinc ion binding / membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | BOS TAURUS (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Standfuss, J. / Edwards, P.C. / Dantona, A. / Fransen, M. / Xie, G. / Oprian, D.D. / Schertler, G.F.X. | |||||||||
Citation | Journal: Nature / Year: 2011 Title: The Structural Basis of Agonist Induced Activation in Constitutively Active Rhodopsin Authors: Standfuss, J. / Edwards, P.C. / Dantona, A. / Fransen, M. / Xie, G. / Oprian, D.D. / Schertler, G.F.X. #1: Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structure of a Thermally Stable Rhodopsin Mutant. Authors: Standfuss, J. / Xie, G. / Edwards, P.C. / Burghammer, M. / Oprian, D.D. / Schertler, G.F.X. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2x72.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2x72.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 2x72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/2x72 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/2x72 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 39033.602 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: RETINA / Cell: ROD PHOTORECEPTOR / Organ: EYE / Cell line (production host): HEK293S GNTI- CELLS / Production host: HOMO SAPIENS (human) / References: UniProt: P02699 |
---|---|
#2: Protein/peptide | Mass: 1265.499 Da / Num. of mol.: 1 / Fragment: RESIDUES 340-350 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) BOS TAURUS (cattle) / References: UniProt: P04695 |
-Sugars , 2 types, 2 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 |
---|---|
#5: Sugar | ChemComp-BOG / |
-Non-polymers , 6 types, 24 molecules
#4: Chemical | ChemComp-PEF / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#6: Chemical | #7: Chemical | ChemComp-RET / | #8: Chemical | ChemComp-LPP / | #9: Chemical | ChemComp-ACT / | #10: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 2 TO CYS ENGINEERED RESIDUE IN CHAIN A, GLU 113 TO GLN ...ENGINEERED |
---|---|
Nonpolymer details | 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE (LPP): PARTIALLY DISORDERED N- ...2-(HEXADECANO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 7.62 Å3/Da / Density % sol: 81.7 % / Description: NONE |
---|---|
Crystal grow | pH: 4.5 Details: 3.0-3.4 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 25221 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 69.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.1 / % possible all: 65.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DQB AND 1GZM Resolution: 3→39.94 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 25.24 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.21 Å2 / ksol: 0.28 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.4 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→39.94 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|