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Yorodumi- PDB-4dkl: Crystal structure of the mu-opioid receptor bound to a morphinan ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dkl | ||||||
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Title | Crystal structure of the mu-opioid receptor bound to a morphinan antagonist | ||||||
Components | Mu-type opioid receptor, lysozyme chimera | ||||||
Keywords | SIGNALING PROTEIN/ANTAGONIST / G-protein coupled receptor / 7 transmembrane receptor / SIGNALING PROTEIN-ANTAGONIST complex | ||||||
Function / homology | Function and homology information Opioid Signalling / spine apparatus / beta-endorphin receptor activity / morphine receptor activity / negative regulation of Wnt protein secretion / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / adenylate cyclase-inhibiting opioid receptor signaling pathway / positive regulation of appetite / G-protein activation ...Opioid Signalling / spine apparatus / beta-endorphin receptor activity / morphine receptor activity / negative regulation of Wnt protein secretion / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / adenylate cyclase-inhibiting opioid receptor signaling pathway / positive regulation of appetite / G-protein activation / G protein-coupled opioid receptor activity / filamin binding / G protein-coupled opioid receptor signaling pathway / regulation of cellular response to stress / G alpha (i) signalling events / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / behavioral response to ethanol / negative regulation of nitric oxide biosynthetic process / neuropeptide binding / negative regulation of cAMP-mediated signaling / positive regulation of neurogenesis / eating behavior / negative regulation of cytosolic calcium ion concentration / transmission of nerve impulse / regulation of NMDA receptor activity / neuropeptide signaling pathway / G-protein alpha-subunit binding / GABA-ergic synapse / voltage-gated calcium channel activity / positive regulation of cAMP-mediated signaling / viral release from host cell by cytolysis / sensory perception of pain / dendrite membrane / excitatory postsynaptic potential / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / peptidoglycan catabolic process / locomotory behavior / G protein-coupled receptor activity / adenylate cyclase-activating dopamine receptor signaling pathway / G-protein beta-subunit binding / positive regulation of nitric oxide biosynthetic process / cell wall macromolecule catabolic process / lysozyme / presynaptic membrane / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / perikaryon / postsynaptic membrane / response to ethanol / host cell cytoplasm / positive regulation of ERK1 and ERK2 cascade / endosome / neuron projection / defense response to bacterium / G protein-coupled receptor signaling pathway / axon / protein domain specific binding / focal adhesion / dendrite / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Manglik, A. / Kruse, A.C. / Kobilka, T.S. / Thian, F.S. / Mathiesen, J.M. / Sunahara, R.K. / Pardo, L. / Weis, W.I. / Kobilka, B.K. / Granier, S. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Crystal structure of the {mu}-opioid receptor bound to a morphinan antagonist. Authors: Manglik, A. / Kruse, A.C. / Kobilka, T.S. / Thian, F.S. / Mathiesen, J.M. / Sunahara, R.K. / Pardo, L. / Weis, W.I. / Kobilka, B.K. / Granier, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dkl.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dkl.ent.gz | 158.2 KB | Display | PDB format |
PDBx/mmJSON format | 4dkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/4dkl ftp://data.pdbj.org/pub/pdb/validation_reports/dk/4dkl | HTTPS FTP |
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-Related structure data
Related structure data | 3oduS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52778.922 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: D1020N, C1054T, C1097A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Enterobacteria phage T4 (virus) Gene: Mor, Oprm, Oprm1, E / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P42866, UniProt: P00720, lysozyme |
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-Non-polymers , 7 types, 55 molecules
#2: Chemical | ChemComp-BF0 / | ||||||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CLR / | #5: Chemical | #6: Chemical | ChemComp-1PE / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
-Details
Sequence details | CHAIN A IS AN INTERNAL FUSION OF LYSOZYME (RESIDUES 2-161 OF UNP P00720) BETWEEN RESIDUES 52-263 ...CHAIN A IS AN INTERNAL FUSION OF LYSOZYME (RESIDUES 2-161 OF UNP P00720) BETWEEN RESIDUES 52-263 AND RESIDUES 270-352 OF MU-TYPE OPIOID RECEPTOR (UNP P42866). AN OFFSET OF 1000 HAS BEEN ADDED TO LYSOZYME RESIDUE NUMBERS WITHIN THE COORDINATE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 25 |
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-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.78 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7 Details: 100 mM HEPES, pH 7.0, 300 mM lithium sulfate, 7.5% DMSO, 30-38% PEG400 in monoolein:cholesterol mixed in a 10:1 ratio, LIPIDIC CUBIC PHASE, temperature 293K |
-Data collection
Diffraction | Mean temperature: 78 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 30, 2011 / Details: Mirrors |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30.5 Å / Num. obs: 19145 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1907 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ODU Resolution: 2.8→30.488 Å / SU ML: 0.86 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.73 / 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: 59.885 Å2 / ksol: 0.319 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→30.488 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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