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- PDB-4ej4: Structure of the delta opioid receptor bound to naltrindole -

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Basic information

Entry
Database: PDB / ID: 4ej4
TitleStructure of the delta opioid receptor bound to naltrindole
ComponentsDelta-type opioid receptor, Lysozyme chimera
KeywordsSIGNALING PROTEIN / Hydrolase/Antagonist / G-protein coupled receptor / 7 transmembrane receptor / opioid receptor / Hydrolase-Antagonist complex
Function / homology
Function and homology information


G protein-coupled enkephalin receptor activity / spine apparatus / Peptide ligand-binding receptors / G protein-coupled opioid receptor activity / G protein-coupled opioid receptor signaling pathway / G alpha (i) signalling events / cellular response to toxic substance / receptor serine/threonine kinase binding / neuropeptide binding / eating behavior ...G protein-coupled enkephalin receptor activity / spine apparatus / Peptide ligand-binding receptors / G protein-coupled opioid receptor activity / G protein-coupled opioid receptor signaling pathway / G alpha (i) signalling events / cellular response to toxic substance / receptor serine/threonine kinase binding / neuropeptide binding / eating behavior / neuronal dense core vesicle / regulation of calcium ion transport / neuropeptide signaling pathway / negative regulation of protein-containing complex assembly / viral release from host cell by cytolysis / axon terminus / dendrite membrane / peptidoglycan catabolic process / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adult locomotory behavior / regulation of mitochondrial membrane potential / response to nicotine / postsynaptic density membrane / cellular response to growth factor stimulus / synaptic vesicle membrane / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / positive regulation of peptidyl-serine phosphorylation / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / cellular response to hypoxia / postsynaptic membrane / vesicle / host cell cytoplasm / defense response to bacterium / neuron projection / negative regulation of gene expression / membrane / plasma membrane
Similarity search - Function
Delta 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 / Phage lysozyme ...Delta 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 / Phage lysozyme / Lysozyme domain superfamily / 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
Chem-EJ4 / Endolysin / Delta-type opioid receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsGranier, S. / Manglik, A. / Kruse, A.C. / Kobilka, T.S. / Thian, F.S. / Weis, W.I. / Kobilka, B.K.
CitationJournal: Nature / Year: 2012
Title: Structure of the delta opioid receptor bound to naltrindole
Authors: Granier, S. / Manglik, A. / Kruse, A.C. / Kobilka, T.S. / Thian, F.S. / Weis, W.I. / Kobilka, B.K.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: Delta-type opioid receptor, Lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0482
Polymers51,6341
Non-polymers4141
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.278, 73.278, 266.653
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Delta-type opioid receptor, Lysozyme chimera / D-OR-1 / DOR-1 / K56 / MSL-2 / Endolysin / Lysis protein / Muramidase


Mass: 51633.738 Da / Num. of mol.: 1 / Fragment: P32300 residues 36-244, 251-342 / Mutation: D1020N, C1054T, C1097A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: Oprd1, E / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P32300, UniProt: P00720, lysozyme
#2: Chemical ChemComp-EJ4 / (4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol / Naltrindole


Mass: 414.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26N2O3 / Comment: antagonist*YM
Has protein modificationY
Sequence detailsCHAIN A IS AN INTERNAL FUSION OF LYSOZYME (RESIDUES 2-161 OF UNP P00720) BETWEEN RESIDUES 36-244 ...CHAIN A IS AN INTERNAL FUSION OF LYSOZYME (RESIDUES 2-161 OF UNP P00720) BETWEEN RESIDUES 36-244 AND RESIDUES 251-342 OF DELTA-TYPE OPIOID RECEPTOR (UNP P32300). AN OFFSET OF 1000 HAS BEEN ADDED TO LYSOZYME RESIDUE NUMBERS WITHIN THE COORDINATES TO DISTINGUISH THAT PORTION OF CHAIN A. LYSOZYME RESIDUES ARE THEREFORE NUMBERED 1002-1161.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 20

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.27 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 29-33% PEG 400, 100 mM HEPES pH 7.5, 120-180 mM sodium citrate, 350 mM Magnesium chloride. Protein was mixed 1:1.5 (w:w) with 91% monoolein 9% cholesterol mixture by weight, Lipidic cubic phase, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1781
2781
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDMar 16, 2012mirrors
MARMOSAIC 300 mm CCD2CCDApr 1, 2012mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.4→40 Å / Num. obs: 12144 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 7.9
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.8 / Num. unique all: 961 / % possible all: 95.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DKL

4dkl


Resolution: 3.4→36.403 Å / SU ML: 1.02 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 28.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2818 1186 9.95 %Random
Rwork0.2522 ---
obs0.2552 11916 98.25 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.535 Å2 / ksol: 0.282 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.6317 Å2-0 Å2-0 Å2
2--12.6317 Å20 Å2
3----25.2634 Å2
Refinement stepCycle: LAST / Resolution: 3.4→36.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 31 0 3382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063464
X-RAY DIFFRACTIONf_angle_d1.0964751
X-RAY DIFFRACTIONf_dihedral_angle_d13.2981187
X-RAY DIFFRACTIONf_chiral_restr0.075579
X-RAY DIFFRACTIONf_plane_restr0.005581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.55490.39741400.37591263X-RAY DIFFRACTION96
3.5549-3.74220.35121450.32721295X-RAY DIFFRACTION96
3.7422-3.97640.31911460.28621307X-RAY DIFFRACTION98
3.9764-4.28290.26391500.24391334X-RAY DIFFRACTION99
4.2829-4.71310.23971440.21951335X-RAY DIFFRACTION99
4.7131-5.39320.28621460.20831349X-RAY DIFFRACTION99
5.3932-6.78770.32651490.2731371X-RAY DIFFRACTION99
6.7877-36.4030.23541660.22361476X-RAY DIFFRACTION99

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