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- PDB-4n6h: 1.8 A Structure of the human delta opioid 7TM receptor (PSI Commu... -

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Basic information

Entry
Database: PDB / ID: 4n6h
Title1.8 A Structure of the human delta opioid 7TM receptor (PSI Community Target)
ComponentsSoluble cytochrome b562, Delta-type opioid receptor chimeric protein
KeywordsSIGNALING PROTEIN / human opioid receptor / sodium regulation / allostery / functional selectivity / GPCR signaling / constitutive activity / GPCR network / membrane protein / PSI-Biology / Structural Genomics / GPCR / membrane
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 / electron transport chain / 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 / cellular response to hypoxia / G alpha (i) signalling events / Interleukin-4 and Interleukin-13 signaling / periplasmic space / electron transfer activity / neuron projection / iron ion binding / immune response / G protein-coupled receptor signaling pathway / negative regulation of gene expression / heme binding / plasma membrane
Similarity search - Function
Delta opioid receptor / Opioid receptor / Cytochrome c/b562 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Delta opioid receptor / Opioid receptor / Cytochrome c/b562 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EJ4 / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / TRIETHYLENE GLYCOL / L(+)-TARTARIC ACID / Soluble cytochrome b562 / Delta-type opioid receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFenalti, G. / Giguere, P.M. / Katritch, V. / Huang, X.-P. / Thompson, A.A. / Han, G.W. / Cherezov, V. / Roth, B.L. / Stevens, R.C. / GPCR Network (GPCR)
CitationJournal: Nature / Year: 2014
Title: Molecular control of delta-opioid receptor signalling.
Authors: Fenalti, G. / Giguere, P.M. / Katritch, V. / Huang, X.P. / Thompson, A.A. / Cherezov, V. / Roth, B.L. / Stevens, R.C.
History
DepositionOct 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Mar 5, 2014Group: Database references / Structure summary
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Soluble cytochrome b562, Delta-type opioid receptor chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,08824
Polymers45,8781
Non-polymers6,21023
Water1,820101
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.230, 72.851, 84.408
Angle α, β, γ (deg.)90.00, 107.48, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Soluble cytochrome b562, Delta-type opioid receptor chimeric protein / D-OR-1 / DOR-1


Mass: 45878.055 Da / Num. of mol.: 1
Fragment: UNP P0ABE7 residues 23-128, UNP P41143 residues 36-338
Mutation: M1007W, H1102I, R1106L, P37S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: OPRD, OPRD1 / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P0ABE7, UniProt: P41143

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Non-polymers , 7 types, 124 molecules

#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: 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
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 47

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 293 K / Method: lcp
Details: 31-34% (v/v) PEG 400, 0.095 to 0.12 M K/Na tartrate, 5% (v/v) ethylene glycol, 100 mM MES buffer at pH 6.1-6.2, LCP, temperature 293K
PH range: 6.1-6.2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDApr 20, 2013mirrors
MARMOSAIC 300 mm CCD2CCDJun 16, 2013mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 45488 / % possible obs: 98.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 2.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EJ4

4ej4


Resolution: 1.8→29.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.568 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REFINEMENT REMARKS: THERE ARE SOME UNKNOWN DENSITIES LOCATED NEAR THE LIGAND BINDING SITE. THEY HAVE NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19028 2303 5.1 %RANDOM
Rwork0.17175 ---
obs0.17271 43157 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.313 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å20.03 Å2
2---0.41 Å2-0 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 341 101 3531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023541
X-RAY DIFFRACTIONr_bond_other_d0.0010.023611
X-RAY DIFFRACTIONr_angle_refined_deg1.4192.0454750
X-RAY DIFFRACTIONr_angle_other_deg0.8513.0038321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8525422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63622.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93515535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7471516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 171 -
Rwork0.247 3042 -
obs--95.85 %
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)
10.34440.04770.07410.65880.20690.6698-0.0226-0.0115-0.0199-0.048-0.07210.04740.0507-0.01060.09480.0339-0.01740.0060.0364-0.00170.0962-8.9959-76.804381.263
20.9849-0.2111.01880.3599-0.49992.7845-0.0743-0.0170.0353-0.0051-0.05710.1218-0.2915-0.0250.13140.0584-0.0058-0.0370.0813-0.00750.1265-16.3698-65.793278.0154
32.08840.48643.75090.28690.18859.7128-0.0116-0.1624-0.06350.0277-0.0737-0.0645-0.2435-0.07950.08520.0381-0.0254-0.02040.06750.01580.1328-0.9442-58.914387.3015
41.00020.2074-0.39950.701-0.22421.816-0.045-0.0429-0.0551-0.0622-0.0825-0.22780.0940.09290.12750.0203-0.00690.01170.05320.01320.1491.4619-70.997280.8764
54.79184.6555-2.95045.4607-2.19332.6758-0.07660.0649-0.19370.09310.018-0.19660.0090.06030.05860.1111-0.0131-0.00390.14290.00980.1624-7.0092-85.0311100.4162
614.984910.25344.651911.6274-2.77839.16880.2291-0.95260.46140.6306-0.35680.3183-0.6032-0.60320.12780.1905-0.14010.06350.4798-0.14890.05125.8891-79.171944.4659
75.71375.83153.44067.17982.71215.27410.4666-0.74020.29420.5084-0.3440.3522-0.2418-0.5618-0.12250.1424-0.07410.04830.2543-0.03760.11490.7476-83.823234.9878
88.67270.6953-2.17222.61160.07084.13410.0401-0.76870.27540.6093-0.0244-0.00480.35020.4335-0.01570.2732-0.1523-0.06150.48290.04070.20322.5178-76.464443.1862
96.44933.01121.91312.1627-0.76594.64450.1975-0.1137-0.12690.0371-0.01040.02590.08220.0082-0.18710.0315-0.0399-0.01680.07220.02290.11924.9625-88.256828.2689
105.79362.77115.80425.04244.04414.04370.6657-0.7299-0.3790.7156-0.64750.12611.1596-0.0004-0.01820.1417-0.0962-0.01580.28120.08330.11412.4431-88.396840.4387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 153
2X-RAY DIFFRACTION2A154 - 207
3X-RAY DIFFRACTION3A208 - 248
4X-RAY DIFFRACTION4A249 - 319
5X-RAY DIFFRACTION5A320 - 338
6X-RAY DIFFRACTION6A1002 - 1012
7X-RAY DIFFRACTION7A1013 - 1043
8X-RAY DIFFRACTION8A1044 - 1063
9X-RAY DIFFRACTION9A1064 - 1089
10X-RAY DIFFRACTION10A1090 - 1106

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