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- PDB-4djh: Structure of the human kappa opioid receptor in complex with JDTic -

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Basic information

Entry
Database: PDB / ID: 4djh
TitleStructure of the human kappa opioid receptor in complex with JDTic
ComponentsKappa-type opioid receptor, Lysozyme
KeywordsHormone 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 / negative regulation of luteinizing hormone secretion / positive regulation of eating behavior / sensory perception of temperature stimulus / adenylate cyclase-inhibiting opioid receptor signaling pathway / G protein-coupled opioid receptor activity / conditioned place preference / G protein-coupled opioid receptor signaling pathway ...dynorphin receptor activity / response to acrylamide / regulation of saliva secretion / negative regulation of luteinizing hormone secretion / positive regulation of eating behavior / sensory perception of temperature stimulus / adenylate cyclase-inhibiting opioid receptor signaling pathway / G protein-coupled opioid receptor activity / conditioned place preference / G protein-coupled opioid receptor signaling pathway / positive regulation of dopamine secretion / positive regulation of potassium ion transmembrane transport / sensory perception / maternal behavior / neuropeptide binding / receptor serine/threonine kinase binding / positive regulation of p38MAPK cascade / eating behavior / behavioral response to cocaine / estrous cycle / neuropeptide signaling pathway / axon terminus / MECP2 regulates neuronal receptors and channels / sensory perception of pain / viral release from host cell by cytolysis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / peptidoglycan catabolic process / locomotory behavior / cellular response to glucose stimulus / response to insulin / synaptic vesicle membrane / response to estrogen / cell wall macromolecule catabolic process / presynaptic membrane / lysozyme / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / perikaryon / chemical synaptic transmission / postsynaptic membrane / defense response to virus / response to ethanol / cellular response to lipopolysaccharide / host cell cytoplasm / neuron projection / defense response to bacterium / immune response / dendrite / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Kappa opioid receptor / Opioid receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme ...Kappa opioid receptor / Opioid receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / 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) / Lysozyme-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Chem-JDC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Endolysin / Kappa-type opioid receptor
Similarity search - Component
Biological speciesHomo Sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWu, 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)
CitationJournal: 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
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Aug 8, 2012Group: Database references / Structure summary
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kappa-type opioid receptor, Lysozyme
B: Kappa-type opioid receptor, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6309
Polymers108,5812
Non-polymers2,0497
Water45025
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-23 kcal/mol
Surface area44690 Å2
MethodPISA
2
B: Kappa-type opioid receptor, Lysozyme
hetero molecules

A: Kappa-type opioid receptor, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6309
Polymers108,5812
Non-polymers2,0497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area2730 Å2
ΔGint-17 kcal/mol
Surface area44330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.896, 147.297, 205.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe dimeric quaternary structure has not been confirmed experimentally

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Components

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Protein , 1 types, 2 molecules AB

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


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 ChemComp-JDC / (3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3,4-tetrahydroisoquinoline-3-carboxamide / JDTic


Mass: 465.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H39N3O3 / Comment: antagonist*YM
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 60

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Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.82 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: 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
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.9→3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.3 / % possible all: 87.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod 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.

3odu

2rh1

3eml

3odu

3pbl

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
RfactorNum. reflection% reflection
Rfree0.2646 1851 5 %
Rwork0.2266 --
obs0.2285 37023 97.8 %
Solvent computationShrinkage 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
Baniso -1Baniso -2Baniso -3
1-6.5962 Å2-0 Å2-0 Å2
2---2.379 Å20 Å2
3----4.2172 Å2
Refinement stepCycle: LAST / Resolution: 2.9→35.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 0 132 25 7089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057218
X-RAY DIFFRACTIONf_angle_d0.7679833
X-RAY DIFFRACTIONf_dihedral_angle_d13.1682521
X-RAY DIFFRACTIONf_chiral_restr0.0391179
X-RAY DIFFRACTIONf_plane_restr0.0031200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.00360.48461560.37633245X-RAY DIFFRACTION92
3.0036-3.12380.33731720.31883416X-RAY DIFFRACTION96
3.1238-3.26590.34831940.26923480X-RAY DIFFRACTION98
3.2659-3.43790.3121910.26273504X-RAY DIFFRACTION99
3.4379-3.65310.29961970.24753522X-RAY DIFFRACTION99
3.6531-3.93490.281880.21433553X-RAY DIFFRACTION99
3.9349-4.33020.22871790.21033534X-RAY DIFFRACTION99
4.3302-4.95540.2231890.19373590X-RAY DIFFRACTION99
4.9554-6.2380.25722000.22683569X-RAY DIFFRACTION98
6.238-35.86420.22921850.2033759X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0389-0.41190.46912.6631.1810.7683-0.09590.09730.12020.08760.0754-0.31030.38140.26410.04220.69720.0246-0.00770.4607-0.03320.40094.6371-21.154849.2538
22.2730.26420.23352.7927-1.46614.51690.0841-0.723-0.38960.2728-0.04170.2822-0.2846-0.0690.02370.34920.0214-0.00020.88540.07580.5481-24.5103-10.57593.3733
34.0035-0.15250.44813.08690.1481.1365-0.11140.4115-0.03330.0448-0.05590.17071.0484-0.19770.1950.6302-0.08230.00970.3994-0.00130.5035-3.3462-26.716643.8287
41.9258-0.21940.79022.7825-0.30371.5448-0.1406-0.29330.17680.80080.0396-0.0401-0.438-0.29960.1120.6386-0.0004-0.04160.42330.01960.34262.8313-64.087649.7661
52.701-0.66871.38832.2448-1.35542.9089-0.0510.42670.2116-0.25010.0658-0.0091-0.0141-0.2441-0.00610.37880.01760.0240.89630.03550.416936.1971-64.42327.5263
63.4196-0.33870.51932.733-1.11854.2934-0.10990.27150.23060.38510.093-0.0933-1.23160.31290.00410.7469-0.099-0.11130.45320.02140.653310.2808-57.490144.8133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 55:261)
2X-RAY DIFFRACTION2(chain A and resid 1002:1161)
3X-RAY DIFFRACTION3(chain A and resid 263:347)
4X-RAY DIFFRACTION4(chain B and resid 55:261)
5X-RAY DIFFRACTION5(chain B and resid 1002:1161)
6X-RAY DIFFRACTION6(chain B and resid 263:347)

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