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- PDB-6pt2: Crystal structure of the active delta opioid receptor in complex ... -

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Basic information

Entry
Database: PDB / ID: 6pt2
TitleCrystal structure of the active delta opioid receptor in complex with the peptide agonist KGCHM07
Components
  • Delta opioid receptor
  • Peptide agonist KGCHM07
KeywordsMEMBRANE PROTEIN/AGONIST / Membrane protein / G protein-coupled receptor / GPCR / DOP / DOR / peptide agonist / active DOP-KGCHM07 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
CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Delta-type opioid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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
Revision 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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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
C: Peptide agonist KGCHM07
D: Peptide agonist KGCHM07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,48613
Polymers103,7664
Non-polymers2,7209
Water543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-52 kcal/mol
Surface area38230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.960, 140.880, 158.640
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

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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: Protein/peptide Peptide agonist KGCHM07


Mass: 823.848 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 12 molecules

#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 27-32% PEG400, 100-120 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: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.51 Å / Num. obs: 26051 / % possible obs: 93.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.9
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.804 / Num. unique obs: 3196

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N6H

4n6h


Resolution: 2.8→49.51 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 1.166 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.117 / SU Rfree Blow DPI: 0.378 / SU Rfree Cruickshank DPI: 0.385
Details: THERE ARE SOME UNKNOWN DENSITIES LOCATED NEAR THE TWO FOLD OF THE MOLECULE CLOSE TO THE SIDE CHAIN OF 152 HIS OF BOTH A AND B CHAINS. THEY HAVE NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1269 4.87 %RANDOM
Rwork0.246 ---
obs0.247 26050 93.2 %-
Displacement parametersBiso max: 236.19 Å2 / Biso mean: 115.43 Å2 / Biso min: 66.85 Å2
Baniso -1Baniso -2Baniso -3
1--19.3644 Å20 Å20 Å2
2--19.4171 Å20 Å2
3----0.0527 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 2.8→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5717 0 252 3 5972
Biso mean--104.29 77.74 -
Num. residues----758
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2014SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes970HARMONIC5
X-RAY DIFFRACTIONt_it6086HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion844SEMIHARMONIC5
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_contact7169SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6086HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8290HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion19.09
LS refinement shellResolution: 2.8→2.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2913 119 4.84 %
Rwork0.2397 2342 -
all0.2421 2461 -
obs--78.83 %
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)
10.83510.1331-0.18960.7218-0.17262.6074-0.1301-0.00030.0388-0.21320.0044-0.02110.09130.14460.12580.05710.02530.0029-0.299-0.0742-0.3257-21.441536.1495-30.5762
20.51870.00220.33931.6784-0.41392.0434-0.1879-0.0552-0.0197-0.04670.1469-0.2479-0.2212-0.03480.0410.12970.02770.0381-0.3174-0.0271-0.3269-22.61416.4206-40.0551
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|1002 - B|1104 B|1107 - B|1399 }B1002 - 1104
4X-RAY DIFFRACTION2{ B|1002 - B|1104 B|1107 - B|1399 }B1107 - 1399

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