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- PDB-6pt3: Crystal structure of the active delta opioid receptor in complex ... -

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Basic information

Entry
Database: PDB / ID: 6pt3
TitleCrystal structure of the active delta opioid receptor in complex with the small molecule agonist DPI-287
ComponentsDelta opioid receptor
KeywordsMEMBRANE PROTEIN/AGONIST / Membrane protein / G protein-coupled receptor / GPCR / DOP / DOR / agonist / active DOP-DPI-287 structure / LCP / MEMBRANE PROTEIN-AGONIST complex
Function / homology
Function and homology information


G protein-coupled enkephalin receptor activity / spine apparatus / positive regulation of CREB transcription factor activity / G protein-coupled opioid receptor activity / G protein-coupled opioid receptor signaling pathway / cellular response to toxic substance / receptor serine/threonine kinase binding / neuropeptide binding / eating behavior / neuronal dense core vesicle ...G protein-coupled enkephalin receptor activity / spine apparatus / positive regulation of CREB transcription factor activity / G protein-coupled opioid receptor activity / G protein-coupled opioid receptor signaling pathway / cellular response to toxic substance / receptor serine/threonine kinase binding / neuropeptide binding / eating behavior / neuronal dense core vesicle / regulation of calcium ion transport / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / neuropeptide signaling pathway / negative regulation of protein-containing complex assembly / axon terminus / dendrite membrane / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / adult locomotory behavior / regulation of mitochondrial membrane potential / postsynaptic density membrane / response to nicotine / cellular response to growth factor stimulus / synaptic vesicle membrane / positive regulation of peptidyl-serine phosphorylation / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / cellular response to hypoxia / Interleukin-4 and Interleukin-13 signaling / neuron projection / immune response / G protein-coupled receptor signaling pathway / negative regulation of gene expression / plasma membrane
Similarity search - Function
Delta opioid receptor / Opioid receptor / 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
Chem-OWY / Delta-type opioid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsClaff, T. / Yu, J. / Blais, V. / Patel, N. / Martin, C. / Wu, L. / Han, G.W. / Holleran, B.J. / Van der Poorten, O. / Hanson, M.A. ...Claff, T. / Yu, J. / Blais, V. / Patel, N. / Martin, C. / Wu, L. / Han, G.W. / Holleran, B.J. / Van der Poorten, O. / Hanson, M.A. / Sarret, P. / Gendron, L. / Cherezov, V. / Katritch, V. / Ballet, S. / Liu, Z. / Muller, C.E. / Stevens, R.C.
CitationJournal: Sci Adv / Year: 2019
Title: Elucidating the active delta-opioid receptor crystal structure with peptide and small-molecule agonists.
Authors: Claff, T. / Yu, J. / Blais, V. / Patel, N. / Martin, C. / Wu, L. / Han, G.W. / Holleran, B.J. / Van der Poorten, O. / White, K.L. / Hanson, M.A. / Sarret, P. / Gendron, L. / Cherezov, V. / ...Authors: Claff, T. / Yu, J. / Blais, V. / Patel, N. / Martin, C. / Wu, L. / Han, G.W. / Holleran, B.J. / Van der Poorten, O. / White, K.L. / Hanson, M.A. / Sarret, P. / Gendron, L. / Cherezov, V. / Katritch, V. / Ballet, S. / Liu, Z.J. / Muller, C.E. / Stevens, R.C.
History
DepositionJul 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Delta opioid receptor
B: Delta opioid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0904
Polymers102,1182
Non-polymers9712
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-22 kcal/mol
Surface area37800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.084, 142.101, 157.491
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Delta opioid receptor


Mass: 51059.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41143*PLUS
#2: Chemical ChemComp-OWY / 4-[(R)-[(2S,5R)-4-benzyl-2,5-dimethylpiperazin-1-yl](3-hydroxyphenyl)methyl]-N,N-diethylbenzamide


Mass: 485.660 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H39N3O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 32-35% PEG400, 100-110 mM potassium citrate tribasic monohydrate and 100 mM MES pH 6.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→49.24 Å / Num. obs: 16342 / % possible obs: 94.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.67
Reflection shellResolution: 3.3→3.39 Å / Rmerge(I) obs: 0.889 / Num. unique obs: 2087

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4n6h

4n6h


Resolution: 3.3→49.24 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.526
Details: THERE ARE SOME UNKNOWN DENSITIES LOCATED NEAR THE LIGAND BINDING SITE ON BOTH A AND B CHAINS THEY HAVE NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 781 4.78 %RANDOM
Rwork0.245 ---
obs0.246 16341 94.5 %-
Displacement parametersBiso max: 244.23 Å2 / Biso mean: 133.77 Å2 / Biso min: 87.12 Å2
Baniso -1Baniso -2Baniso -3
1--23.3867 Å20 Å20 Å2
2--23.348 Å20 Å2
3---0.0387 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: final / Resolution: 3.3→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5646 0 72 0 5718
Biso mean--111.03 --
Num. residues----752
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2597SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes859HARMONIC5
X-RAY DIFFRACTIONt_it5846HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion835SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7233SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5846HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7996HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion2.2
X-RAY DIFFRACTIONt_other_torsion3.02
LS refinement shellResolution: 3.3→3.53 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.268 131 5 %
Rwork0.237 2488 -
all0.239 2619 -
obs--85.5 %
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)
11.0786-0.18570.56530.7152-0.50713.5057-0.15650.0262-0.06980.2453-0.00580.011-0.13920.16810.16240.0501-0.00790.0587-0.2649-0.1155-0.28192.9942-36.3644-48.5911
20.6052-0.0348-0.84722.2251-0.08091.8512-0.17120.08750.02440.12730.1212-0.25160.1610.18720.050.1684-0.0038-0.0862-0.3026-0.0242-0.31092.2154-5.7961-40.2
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|999 - A|1106 A|41 - A|329 }A999 - 1106
2X-RAY DIFFRACTION1{ A|999 - A|1106 A|41 - A|329 }A41 - 329
3X-RAY DIFFRACTION2{ B|1003 - B|1100 B|1110 - B|1400 }B1003 - 1100
4X-RAY DIFFRACTION2{ B|1003 - B|1100 B|1110 - B|1400 }B1110 - 1400

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