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- PDB-5dhh: The crystal structure of nociceptin/orphanin FQ peptide receptor ... -

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Basic information

Entry
Database: PDB / ID: 5dhh
TitleThe crystal structure of nociceptin/orphanin FQ peptide receptor (NOP) in complex with SB-612111 (PSI Community Target)
ComponentsSoluble cytochrome b562,Nociceptin receptor
KeywordsSIGNALING PROTEIN / Nociceptin/orphanin FQ peptide receptor / NOP / ORL-1 / N/OFQ / opioid receptor / G protein-coupled receptor / GPCR / membrane protein / lipidic cubic phase / BRET / receptor-ligand conformational pair / Structural Genomics / PSI-Biology / GPCR Network / PSICNT-127
Function / homology
Function and homology information


nociceptin receptor activity / regulation of locomotor rhythm / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / sensory perception / positive regulation of urine volume / conditioned place preference / neuropeptide binding / eating behavior / negative regulation of cAMP-mediated signaling / neuropeptide signaling pathway ...nociceptin receptor activity / regulation of locomotor rhythm / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / sensory perception / positive regulation of urine volume / conditioned place preference / neuropeptide binding / eating behavior / negative regulation of cAMP-mediated signaling / neuropeptide signaling pathway / estrous cycle / negative regulation of blood pressure / sensory perception of pain / Peptide ligand-binding receptors / calcium-mediated signaling / electron transport chain / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / response to estradiol / cytoplasmic vesicle / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / electron transfer activity / periplasmic space / neuron projection / iron ion binding / heme binding / plasma membrane
Similarity search - Function
X opioid receptor / Opioid receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...X opioid receptor / Opioid receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DGW / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / Nociceptin receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsMiller, R.L. / Thompson, A.A. / Trapella, C. / Guerrini, R. / Malfacini, D. / Patel, N. / Han, G.W. / Cherezov, V. / Calo, G. / Katritch, V. ...Miller, R.L. / Thompson, A.A. / Trapella, C. / Guerrini, R. / Malfacini, D. / Patel, N. / Han, G.W. / Cherezov, V. / Calo, G. / Katritch, V. / Stevens, R.C. / GPCR Network (GPCR)
CitationJournal: Structure / Year: 2015
Title: The Importance of Ligand-Receptor Conformational Pairs in Stabilization: Spotlight on the N/OFQ G Protein-Coupled Receptor.
Authors: Miller, R.L. / Thompson, A.A. / Trapella, C. / Guerrini, R. / Malfacini, D. / Patel, N. / Han, G.W. / Cherezov, V. / Calo, G. / Katritch, V. / Stevens, R.C.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3May 31, 2017Group: Source and taxonomy
Revision 1.4Jul 5, 2017Group: Database references / Category: struct_ref_seq / Item: _struct_ref_seq.pdbx_auth_seq_align_beg
Revision 1.5Sep 27, 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 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562,Nociceptin receptor
B: Soluble cytochrome b562,Nociceptin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,56312
Polymers93,3932
Non-polymers3,17110
Water00
1
A: Soluble cytochrome b562,Nociceptin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5277
Polymers46,6961
Non-polymers1,8316
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Soluble cytochrome b562,Nociceptin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0365
Polymers46,6961
Non-polymers1,3404
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Soluble cytochrome b562,Nociceptin receptor
hetero molecules

B: Soluble cytochrome b562,Nociceptin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,56312
Polymers93,3932
Non-polymers3,17110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3670 Å2
ΔGint-7 kcal/mol
Surface area32980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.300, 168.941, 65.472
Angle α, β, γ (deg.)90.00, 103.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Soluble cytochrome b562,Nociceptin receptor / Cytochrome b-562 / Kappa-type 3 opioid receptor / KOR-3 / Orphanin FQ receptor


Mass: 46696.371 Da / Num. of mol.: 2 / Mutation: M1007W, H1102I, R1106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Strain: O26:H11 / Gene: cybC, OPRL1, OOR, ORL1 / Plasmid: pFASTBAC / Cell line (production host): sf9 / Production host: spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P0ABE7, UniProt: P41146
#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-DGW / (5S,7S)-7-{[4-(2,6-dichlorophenyl)piperidin-1-yl]methyl}-1-methyl-6,7,8,9-tetrahydro-5H-benzo[7]annulen-5-ol


Mass: 418.399 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H29Cl2NO / Comment: antidepressant, antagonist*YM
#4: 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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.4
Details: 25-35% (V/V) PEG400, 130-200 MM POTASSIM SODIUM TARTRATE TETRAHYDRATE, 100 MM BIS-TRIS PROPANE, PH 6.4, 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 8, 2013 / Details: Another data collection date: 2014-02-20
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 16552 / % possible obs: 93.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 7.27
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.19 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EA3

4ea3


Resolution: 3.004→29.845 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 827 5.01 %
Rwork0.2403 --
obs0.2423 16523 92.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.004→29.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 145 0 5172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045273
X-RAY DIFFRACTIONf_angle_d0.7727178
X-RAY DIFFRACTIONf_dihedral_angle_d13.6813117
X-RAY DIFFRACTIONf_chiral_restr0.043873
X-RAY DIFFRACTIONf_plane_restr0.006881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0042-3.19220.39031330.32192530X-RAY DIFFRACTION91
3.1922-3.43830.34481380.28822614X-RAY DIFFRACTION93
3.4383-3.78370.28391390.25622645X-RAY DIFFRACTION94
3.7837-4.32980.25581400.2112650X-RAY DIFFRACTION94
4.3298-5.44970.2671380.22792631X-RAY DIFFRACTION94
5.4497-29.84680.2491390.22372626X-RAY DIFFRACTION92
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)
10.2969-0.09710.23030.168-0.04790.4427-0.07470.05810.0440.04150.0338-0.02080.0335-0.027-00.2681-0.0071-0.0090.270.03060.2876-8.314341.2773-0.1447
20.1259-0.0937-0.08310.00550.03950.5213-0.0427-0.1283-0.0162-0.01090.0544-0.0062-0.0023-0.049800.14560.01610.00820.2205-0.00450.1666-13.807732.6253-39.968
30.0510.00570.05450.0280.0955-0.03860.29740.3948-0.00720.1715-0.36050.0182-0.1273-0.391500.6782-0.0116-0.01430.5056-0.2360.6524-31.204876.986-25.2503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 332)
2X-RAY DIFFRACTION2chain 'B' and (resid 44 through 334)
3X-RAY DIFFRACTION3chain 'B' and (resid 1003 through 1106)

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