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Yorodumi- PDB-4djh: Structure of the human kappa opioid receptor in complex with JDTic -
+Open data
-Basic information
Entry | Database: PDB / ID: 4djh | ||||||
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Title | Structure of the human kappa opioid receptor in complex with JDTic | ||||||
Components | Kappa-type opioid receptor, Lysozyme | ||||||
Keywords | Hormone receptor/antagonist / JDtic / GPCR newtork / PSI-Biology / KOR / hKOR / KOP / Structural Genomics / Protein Structure Initiative / GPCR Network / G-protein coupled receptor / GPCR / 7TM / kappa opioid receptor / dynorphin / membrane protein / transmembrane / Hormone receptor / Hydrolase / Hormone receptor-antagonist complex | ||||||
Function / homology | Function and homology information dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / sensory perception of temperature stimulus / positive regulation of eating behavior / adenylate cyclase-inhibiting opioid receptor signaling pathway / G protein-coupled opioid receptor activity / negative regulation of luteinizing hormone secretion / G protein-coupled opioid receptor signaling pathway / positive regulation of dopamine secretion ...dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / sensory perception of temperature stimulus / positive regulation of eating behavior / adenylate cyclase-inhibiting opioid receptor signaling pathway / G protein-coupled opioid receptor activity / negative regulation of luteinizing hormone secretion / G protein-coupled opioid receptor signaling pathway / positive regulation of dopamine secretion / sensory perception / positive regulation of potassium ion transmembrane transport / conditioned place preference / maternal behavior / receptor serine/threonine kinase binding / neuropeptide binding / positive regulation of p38MAPK cascade / eating behavior / behavioral response to cocaine / neuropeptide signaling pathway / estrous cycle / MECP2 regulates neuronal receptors and channels / axon terminus / viral release from host cell by cytolysis / sensory perception of pain / T-tubule / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / peptidoglycan catabolic process / Peptide ligand-binding receptors / sarcoplasmic reticulum / locomotory behavior / cellular response to glucose stimulus / response to nicotine / response to insulin / synaptic vesicle membrane / response to estrogen / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / cellular response to lipopolysaccharide / chemical synaptic transmission / postsynaptic membrane / perikaryon / response to ethanol / defense response to virus / host cell cytoplasm / defense response to bacterium / neuron projection / immune response / dendrite / mitochondrion / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo Sapiens (human) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Wu, H. / Wacker, D. / Katritch, V. / Mileni, M. / Han, G.W. / Vardy, E. / Liu, W. / Thompson, A.A. / Huang, X.P. / Carroll, F.I. ...Wu, H. / Wacker, D. / Katritch, V. / Mileni, M. / Han, G.W. / Vardy, E. / Liu, W. / Thompson, A.A. / Huang, X.P. / Carroll, F.I. / Mascarella, S.W. / Westkaemper, R.B. / Mosier, P.D. / Roth, B.L. / Cherezov, V. / Stevens, R.C. / GPCR Network (GPCR) | ||||||
Citation | Journal: Nature / Year: 2012 Title: tructure of the human kappa-opioid receptor in complex with JDTic Authors: Wu, H. / Wacker, D. / Mileni, M. / Katritch, V. / Han, G.W. / Vardy, E. / Liu, W. / Thompson, A.A. / Huang, X.P. / Carroll, F.I. / Mascarella, S.W. / Westkaemper, R.B. / Mosier, P.D. / Roth, ...Authors: Wu, H. / Wacker, D. / Mileni, M. / Katritch, V. / Han, G.W. / Vardy, E. / Liu, W. / Thompson, A.A. / Huang, X.P. / Carroll, F.I. / Mascarella, S.W. / Westkaemper, R.B. / Mosier, P.D. / Roth, B.L. / Cherezov, V. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4djh.cif.gz | 371.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4djh.ent.gz | 303 KB | Display | PDB format |
PDBx/mmJSON format | 4djh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/4djh ftp://data.pdbj.org/pub/pdb/validation_reports/dj/4djh | HTTPS FTP |
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-Related structure data
Related structure data | 2rh1S 3emlS 3oduS 3pblS 3rzeS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | the dimeric quaternary structure has not been confirmed experimentally |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54290.480 Da / Num. of mol.: 2 Fragment: UNP P41145 residues 43-261, UNP P00720 residues 2-161, UNP P41145 residues 362-358 Mutation: I135L, C54T, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo Sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: OPRK, OPRK1, OPRK, e / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41145, UniProt: P00720 |
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-Non-polymers , 5 types, 32 molecules
#2: Chemical | #3: Chemical | ChemComp-CIT / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 60 |
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-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.82 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: 100 mM sodium citrate pH 6.0, 30% (v/v) PEG400, 400 mM potassium nitrate, lipidic cubic phase, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 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: Dec 10, 2011 Details: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 38323 / % possible obs: 97.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.3 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: poly Ala model of PDB entry 3ODU. ensemble of T4L models from PDB entries 2RH1, 3EML,3ODU, 3PBL, and 3RZE. Resolution: 2.9→35.861 Å / SU ML: 0.54 / Isotropic thermal model: Isotropic / σ(F): 1.33 / Phase error: 29.47 / Stereochemistry target values: ML Details: THERE ARE SOME UNKNOWN DENSITIES LOCATED NEAR THE LIGAND BINDING SITE AND AT THE END OF THE SIDE CHAIN OF CYS345 ON BOTH A AND B CHAINS. THEY HAVE NOT BEEN MODELLED
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.003 Å2 / ksol: 0.301 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.9→35.861 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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