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

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Basic information

Entry
Database: PDB / ID: 5dhg
TitleThe crystal structure of nociceptin/orphanin FQ peptide receptor (NOP) in complex with C-35 (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 / sensory perception / negative regulation of cAMP-mediated signaling / positive regulation of urine volume / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / conditioned place preference / neuropeptide binding / eating behavior / neuropeptide signaling pathway ...nociceptin receptor activity / regulation of locomotor rhythm / sensory perception / negative regulation of cAMP-mediated signaling / positive regulation of urine volume / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / conditioned place preference / neuropeptide binding / eating behavior / neuropeptide signaling pathway / estrous cycle / negative regulation of blood pressure / sensory perception of pain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor activity / calcium-mediated signaling / electron transport chain / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / cytoplasmic vesicle / periplasmic space / electron transfer activity / 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-DGV / 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 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 30, 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 1.3Mar 2, 2016Group: Database references
Revision 1.4May 31, 2017Group: Source and taxonomy
Revision 1.5Jul 5, 2017Group: Database references / Category: struct_ref_seq / Item: _struct_ref_seq.pdbx_auth_seq_align_beg
Revision 1.6Sep 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 1.7Oct 16, 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)96,11110
Polymers93,3932
Non-polymers2,7188
Water00
1
A: Soluble cytochrome b562,Nociceptin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0185
Polymers46,6961
Non-polymers1,3224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Soluble cytochrome b562,Nociceptin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0925
Polymers46,6961
Non-polymers1,3964
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)96,11110
Polymers93,3932
Non-polymers2,7188
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area2780 Å2
ΔGint-11 kcal/mol
Surface area32700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.079, 171.696, 66.491
Angle α, β, γ (deg.)90.00, 103.25, 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-DGV / 1-benzyl-N-{3-[4-(2,6-dichlorophenyl)piperidin-1-yl]propyl}-D-prolinamide


Mass: 474.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H33Cl2N3O
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H34O2
#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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.033
SYNCHROTRONAPS 23-ID-B21.033
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDDec 8, 2013
MARMOSAIC 300 mm CCD2CCDNov 16, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2mirrorsSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21
ReflectionResolution: 3→30 Å / Num. obs: 16902 / % possible obs: 90.8 % / Redundancy: 3.3 % / Rsym value: 0.192 / Net I/σ(I): 7.77
Reflection shellResolution: 3→3 Å / Redundancy: 3 % / % possible all: 90.6

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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→29.633 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 835 5.01 %Random selection
Rwork0.2354 ---
obs0.2373 16668 90.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4952 0 119 0 5071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045175
X-RAY DIFFRACTIONf_angle_d0.7477062
X-RAY DIFFRACTIONf_dihedral_angle_d12.5593007
X-RAY DIFFRACTIONf_chiral_restr0.044873
X-RAY DIFFRACTIONf_plane_restr0.005864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.18780.36471380.31242622X-RAY DIFFRACTION91
3.1878-3.43360.34511390.28572637X-RAY DIFFRACTION92
3.4336-3.77850.30371420.26882675X-RAY DIFFRACTION92
3.7785-4.32380.26981390.21372658X-RAY DIFFRACTION92
4.3238-5.4420.27011390.21862646X-RAY DIFFRACTION91
5.442-29.63430.23381380.22232595X-RAY DIFFRACTION89
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)
10.087-0.10170.18280.11770.2290.4736-0.0510.0370.0681-0.04850.02770.02670.00180.0418-00.4755-0.01390.00410.47760.03520.4904-8.708843.02650.0502
20.35790.60810.71780.3276-0.62841.0515-0.0385-0.02320.1170.06120.06910.0332-0.0107-0.127300.1024-0.00150.02180.18270.01760.1752-14.338834.7899-40.2993
30.1395-0.05460.01170.09540.08590.08410.24380.0461-0.13440.18-0.30030.20480.08020.063300.960.0434-0.0270.68-0.1380.8163-30.58879.5832-25.7701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 333)
2X-RAY DIFFRACTION2chain 'B' and (resid 44 through 333)
3X-RAY DIFFRACTION3chain 'B' and (resid 1003 through 1106)

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