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- PDB-7yit: Molecular mechanism of biased signaling at the kappa opioid receptor -

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Basic information

Entry
Database: PDB / ID: 7yit
TitleMolecular mechanism of biased signaling at the kappa opioid receptor
Components
  • Kappa-type opioid receptor
  • Nanobody39
  • Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN/INHIBITOR/IMMUNE SYSTEM / Kappa Opioid Receptor / MEMBRANE PROTEIN / nalfurafine / opioids / MEMBRANE PROTEIN-INHIBITOR-IMMUNE SYSTEM complex
Function / homology
Function and homology information


response to acrylamide / regulation of saliva secretion / dynorphin receptor activity / 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 ...response to acrylamide / regulation of saliva secretion / dynorphin receptor activity / 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 / maternal behavior / conditioned place preference / 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 / response to nicotine / electron transport chain / 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 / perikaryon / defense response to virus / postsynaptic membrane / response to ethanol / periplasmic space / electron transfer activity / neuron projection / immune response / iron ion binding / dendrite / heme binding / mitochondrion / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Kappa opioid receptor / Opioid receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
nalfurafine / Soluble cytochrome b562 / Kappa-type opioid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKim, K. / Che, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM143061 United States
CitationJournal: Nat Commun / Year: 2023
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
DepositionJul 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kappa-type opioid receptor
D: Nanobody39
E: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8254
Polymers60,3493
Non-polymers4771
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.750, 76.530, 154.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Kappa-type opioid receptor / K-OR-1 / KOR-1


Mass: 34687.332 Da / Num. of mol.: 1 / Mutation: I135L,S324C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OPRK1, OPRK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41145
#2: Protein Nanobody39


Mass: 13570.950 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 12090.537 Da / Num. of mol.: 1 / Mutation: M1007W,V1084E,H1102I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7
#4: Chemical ChemComp-IVB / nalfurafine / ~{N}-[(4~{R},4~{a}~{S},7~{R},7~{a}~{R},12~{b}~{S})-3-(cyclopropylmethyl)-4~{a},9-bis(oxidanyl)-1,2,4,5,6,7,7~{a},13-octahydro-4,12-methanobenzofuro[3,2-e]isoquinolin-7-yl]-3-(furan-3-yl)-~{N}-methyl-propanamide


Mass: 476.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H32N2O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.75 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 83 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3.3→3.56 Å / Num. unique obs: 1594 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B73

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
RfactorNum. reflection% reflection
Rfree0.3352 1244 10.02 %
Rwork0.2851 11176 -
obs0.2899 12420 94.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 130.81 Å2
Refinement stepCycle: LAST / Resolution: 3.3→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 35 0 3386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00453456
X-RAY DIFFRACTIONf_angle_d0.82044754
X-RAY DIFFRACTIONf_chiral_restr0.0446601
X-RAY DIFFRACTIONf_plane_restr0.0046582
X-RAY DIFFRACTIONf_dihedral_angle_d7.6089498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.430.48491210.42871103X-RAY DIFFRACTION85.59
3.43-3.590.44911320.39821153X-RAY DIFFRACTION88.99
3.59-3.780.43681230.35161171X-RAY DIFFRACTION90.93
3.78-4.010.39391430.31771219X-RAY DIFFRACTION93.48
4.01-4.320.34111300.27771275X-RAY DIFFRACTION97.1
4.32-4.760.34711450.25711270X-RAY DIFFRACTION97.25
4.76-5.440.30721460.26761297X-RAY DIFFRACTION97.96
5.44-6.850.38321450.34151303X-RAY DIFFRACTION98.37
6.85-37.140.27641590.24521385X-RAY DIFFRACTION97.54
Refinement TLS params.Method: refined / Origin x: 17.0017720896 Å / Origin y: 16.977098987 Å / Origin z: 5.50676474267 Å
111213212223313233
T1.21272234949 Å2-0.0212649239291 Å20.0479274005477 Å2-1.01671163001 Å20.0396183364128 Å2--1.02275481129 Å2
L0.468065266806 °20.0729281269411 °2-0.068590368063 °2-0.797256200009 °20.314382265946 °2--0.354124448379 °2
S-0.055411238046 Å °-0.00855830274128 Å °-0.0351967642503 Å °0.0202226992411 Å °-0.00510633175621 Å °-0.0537742290896 Å °0.0824376705096 Å °-0.188997555955 Å °0.0812938109448 Å °
Refinement TLS groupSelection details: all

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