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- PDB-7yit: Molecular mechanism of biased signaling at the kappa opioid receptor -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yit | ||||||
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Title | Molecular mechanism of biased signaling at the kappa opioid receptor | ||||||
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![]() | MEMBRANE PROTEIN/INHIBITOR/IMMUNE SYSTEM / Kappa Opioid Receptor / MEMBRANE PROTEIN / nalfurafine / opioids / MEMBRANE PROTEIN-INHIBITOR-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() 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 / sensory perception of pain / T-tubule / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / sarcoplasmic reticulum / locomotory behavior / cellular response to glucose stimulus / electron transport chain / response to nicotine / response to insulin / synaptic vesicle membrane / response to estrogen / 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 / periplasmic space / electron transfer activity / neuron projection / iron ion binding / immune response / dendrite / heme binding / mitochondrion / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, K. / Che, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism of biased signaling at the kappa opioid receptor. Authors: El Daibani, A. / Paggi, J.M. / Kim, K. / Laloudakis, Y.D. / Popov, P. / Bernhard, S.M. / Krumm, B.E. / Olsen, R.H.J. / Diberto, J. / Carroll, F.I. / Katritch, V. / Wunsch, B. / Dror, R.O. / Che, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.4 KB | Display | ![]() |
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PDB format | ![]() | 147.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6b73S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34687.332 Da / Num. of mol.: 1 / Mutation: I135L,S324C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 13570.950 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 12090.537 Da / Num. of mol.: 1 / Mutation: M1007W,V1084E,H1102I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Chemical | ChemComp-IVB / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.75 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.7 Details: 40-200 mM magnesium sulfate hydrate, 100 mM sodium citrate tribasic dehydrate, 10 mM Manganese (II) chloride tetrahydrate 28-30% PEG400 PH range: 6.5-7.0 |
-Data collection
Diffraction | Mean temperature: 83 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→38.38 Å / Num. obs: 40881 / % possible obs: 94.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 125.38 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.3→3.56 Å / Num. unique obs: 1594 / CC1/2: 0.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6B73 Resolution: 3.3→37.14 Å / SU ML: 0.7198 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 43.3771 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 130.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→37.14 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 17.0017720896 Å / Origin y: 16.977098987 Å / Origin z: 5.50676474267 Å
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Refinement TLS group | Selection details: all |