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- PDB-4a4m: Crystal structure of the light-activated constitutively active N2... -
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Basic information
Entry | Database: PDB / ID: 4a4m | |||||||||
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Title | Crystal structure of the light-activated constitutively active N2C, M257Y,D282C rhodopsin mutant in complex with a peptide resembling the C-terminus of the Galpha-protein subunit (GaCT) | |||||||||
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![]() | SIGNALING PROTEIN / G-PROTEIN / G-PROTEIN-COUPLED RECEPTORS / SIGNAL TANSDUCTION / VISUAL SYSTEM / METARHODOPSIN-II | |||||||||
Function / homology | ![]() Adenylate cyclase inhibitory pathway / detection of light stimulus involved in visual perception / negative regulation of cyclic-nucleotide phosphodiesterase activity / Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / rod photoreceptor outer segment / sperm head plasma membrane / sensory perception of umami taste ...Adenylate cyclase inhibitory pathway / detection of light stimulus involved in visual perception / negative regulation of cyclic-nucleotide phosphodiesterase activity / Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / rod photoreceptor outer segment / sperm head plasma membrane / sensory perception of umami taste / absorption of visible light / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / The canonical retinoid cycle in rods (twilight vision) / sensory perception of sweet taste / : / photoreceptor inner segment membrane / podosome assembly / G protein-coupled opsin signaling pathway / 11-cis retinal binding / G protein-coupled photoreceptor activity / detection of chemical stimulus involved in sensory perception of bitter taste / 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 / ADP signalling through P2Y purinoceptor 12 / Extra-nuclear estrogen signaling / photoreceptor outer segment membrane / G alpha (i) signalling events / phototransduction / photoreceptor outer segment / G-protein alpha-subunit binding / response to light stimulus / acyl 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 / photoreceptor disc membrane / microtubule cytoskeleton organization / 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 / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Deupi, X. / Edwards, P. / Singhal, A. / Nickle, B. / Oprian, D.D. / Schertler, G.F.X. / Standfuss, J. | |||||||||
![]() | ![]() Title: Stabilized G Protein Binding Site in the Structure of Constitutively Active Metarhodopsin-II. Authors: Deupi, X. / Edwards, P. / Singhal, A. / Nickle, B. / Oprian, D. / Schertler, G. / Standfuss, J. #1: ![]() 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. #2: ![]() Title: The Structural Basis of Agonist-Induced Activation in Constitutively Active Rhodopsin. Authors: Standfuss, J. / Edwards, P.C. / D'Antona, A. / Fransen, M. / Xie, G. / Oprian, D.D. / Schertler, G.F.X. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 63.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x72S 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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1 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 39066.562 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1265.499 Da / Num. of mol.: 1 / Fragment: RESIDUES 344-354 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Sugars , 2 types, 2 molecules ![](data/chem/img/BOG.gif)
#3: Polysaccharide | 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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#6: Sugar | ChemComp-BOG / |
-Non-polymers , 4 types, 12 molecules ![](data/chem/img/RET.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-RET / |
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#5: Chemical | ChemComp-ACT / |
#7: Chemical | ChemComp-PLM / |
#8: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 2 TO CYS ENGINEERED RESIDUE IN CHAIN A, MET 257 TO TYR ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.96 Å3/Da / Density % sol: 84.43 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: 3.0-3.4 M AMMONIUM SULPHATE, 100 MM SODIUM ACETATE PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→45 Å / Num. obs: 17649 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 75.56 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.8 / % possible all: 65.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X72 Resolution: 3.3→45.77 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 26.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.896 Å2 / ksol: 0.279 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.3→45.77 Å
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Refine LS restraints |
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LS refinement shell |
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