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Yorodumi- PDB-6b73: Crystal Structure of a nanobody-stabilized active state of the ka... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b73 | ||||||
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Title | Crystal Structure of a nanobody-stabilized active state of the kappa-opioid receptor | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/AGONIST / GPCR / opioid receptor / addiction / active state / nanobody / structure-function / morphinan / LCP / membrane protein / MEMBRANE PROTEIN-AGONIST 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 / 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 | Escherichia coli (E. coli) Homo sapiens (human) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Che, T. / Majumdar, S. / Zaidi, S.A. / Kormos, C. / McCorvy, J.D. / Wang, S. / Mosier, P.D. / Uprety, R. / Vardy, E. / Krumm, B.E. ...Che, T. / Majumdar, S. / Zaidi, S.A. / Kormos, C. / McCorvy, J.D. / Wang, S. / Mosier, P.D. / Uprety, R. / Vardy, E. / Krumm, B.E. / Han, G.W. / Lee, M.Y. / Pardon, E. / Steyaert, J. / Huang, X.P. / Strachan, R.T. / Tribo, A.R. / Pasternak, G.W. / Carroll, I.F. / Stevens, R.C. / Cherezov, V. / Katritch, V. / Wacker, D. / Roth, B.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell / Year: 2018 Title: Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor. Authors: Che, T. / Majumdar, S. / Zaidi, S.A. / Ondachi, P. / McCorvy, J.D. / Wang, S. / Mosier, P.D. / Uprety, R. / Vardy, E. / Krumm, B.E. / Han, G.W. / Lee, M.Y. / Pardon, E. / Steyaert, J. / ...Authors: Che, T. / Majumdar, S. / Zaidi, S.A. / Ondachi, P. / McCorvy, J.D. / Wang, S. / Mosier, P.D. / Uprety, R. / Vardy, E. / Krumm, B.E. / Han, G.W. / Lee, M.Y. / Pardon, E. / Steyaert, J. / Huang, X.P. / Strachan, R.T. / Tribo, A.R. / Pasternak, G.W. / Carroll, F.I. / Stevens, R.C. / Cherezov, V. / Katritch, V. / Wacker, D. / Roth, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b73.cif.gz | 322.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b73.ent.gz | 261.5 KB | Display | PDB format |
PDBx/mmJSON format | 6b73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/6b73 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/6b73 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
-Components
#1: Protein | Mass: 47030.043 Da / Num. of mol.: 2 / Fragment: unp residues 23-128; unp residues 54-358 / Mutation: M29W, H124I, L51R, I135L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: cybC, OPRK1, OPRK / Production host: unidentified baculovirus / References: UniProt: P0ABE7, UniProt: P41145 #2: Antibody | Mass: 14913.330 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Lama glama (llama) #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-OLA / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.4 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100 mM Bis-tris pH 6.5-7.0, 140-200 mM magnesium sulfate hydrate, 100 mM sodium citrate tribasic dehydrate, 10 mM Manganese(II) chloride tetrahydrate, 28-30% PEG400 |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→46.94 Å / Num. obs: 30278 / % possible obs: 93.6 % / Redundancy: 3 % / Biso Wilson estimate: 78.82 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.187 / Net I/σ(I): 4 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4159 / CC1/2: 0.537 / % possible all: 88.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 4DJH, 5C1M, 1M6T Resolution: 3.1→46.94 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.832 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.834 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.714 / SU Rfree Blow DPI: 0.374 / SU Rfree Cruickshank DPI: 0.391 Details: THERE ARE SOME UNKNOWN DENSITIES LOCATED ABOVE THE LIGAND BINDING SITE AND NEAR THE TRP222 ON BOTH A AND B CHAINS. THEY HAVE NOT BEEN MODELLED.
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Displacement parameters | Biso mean: 85.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.6 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.1→46.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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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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