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- PDB-4ea3: Structure of the N/OFQ Opioid Receptor in Complex with a Peptide ... -

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Basic information

Entry
Database: PDB / ID: 4ea3
TitleStructure of the N/OFQ Opioid Receptor in Complex with a Peptide Mimetic
ComponentsFusion protein of Nociceptin receptor and cytochrome b562
KeywordsSIGNALING PROTEIN / PSI-biology GPCR network / Structural Genomics / GPCR membrane protein 7TM NOP ORL1 cytochrome b562 / receptor / nociceptin orphanin FQ compound 24 opioid / fusion / membrane transmembrane
Function / homology
Function and homology information


nociceptin receptor activity / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / conditioned place preference / regulation of locomotor rhythm / sensory perception / positive regulation of urine volume / neuropeptide binding / negative regulation of cAMP-mediated signaling / eating behavior / estrous cycle ...nociceptin receptor activity / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / conditioned place preference / regulation of locomotor rhythm / sensory perception / positive regulation of urine volume / neuropeptide binding / negative regulation of cAMP-mediated signaling / eating behavior / estrous cycle / neuropeptide signaling pathway / sensory perception of pain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / negative regulation of blood pressure / Peptide ligand-binding receptors / G protein-coupled receptor activity / calcium-mediated signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / cytoplasmic vesicle / electron transfer activity / periplasmic space / neuron projection / iron ion binding / heme binding / plasma membrane
Similarity search - Function
X 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) ...X 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-0NN / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (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: 3.013 Å
AuthorsThompson, A.A. / Liu, W. / Chun, E. / Katritch, V. / Wu, H. / Vardy, E. / Huang, X.P. / Trapella, C. / Guerrini, R. / Calo, G. ...Thompson, A.A. / Liu, W. / Chun, E. / Katritch, V. / Wu, H. / Vardy, E. / Huang, X.P. / Trapella, C. / Guerrini, R. / Calo, G. / Roth, B.L. / Cherezov, V. / Stevens, R.C. / GPCR Network (GPCR)
CitationJournal: Nature / Year: 2012
Title: Structure of the nociceptin/orphanin FQ receptor in complex with a peptide mimetic.
Authors: Thompson, A.A. / Liu, W. / Chun, E. / Katritch, V. / Wu, H. / Vardy, E. / Huang, X.P. / Trapella, C. / Guerrini, R. / Calo, G. / Roth, B.L. / Cherezov, V. / Stevens, R.C.
History
DepositionMar 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion protein of Nociceptin receptor and cytochrome b562
B: Fusion protein of Nociceptin receptor and cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0187
Polymers96,1562
Non-polymers1,8635
Water1448
1
A: Fusion protein of Nociceptin receptor and cytochrome b562
hetero molecules

B: Fusion protein of Nociceptin receptor and cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0187
Polymers96,1562
Non-polymers1,8635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area2470 Å2
ΔGint-24 kcal/mol
Surface area32000 Å2
MethodPISA
2
A: Fusion protein of Nociceptin receptor and cytochrome b562
hetero molecules

B: Fusion protein of Nociceptin receptor and cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0187
Polymers96,1562
Non-polymers1,8635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area2790 Å2
ΔGint-21 kcal/mol
Surface area31680 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-18 kcal/mol
Surface area32550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.106, 170.939, 65.353
Angle α, β, γ (deg.)90.00, 103.14, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe significant oligomerization state of the receptor is unknown. Authors state that the configuration cannot occur in an anti-parallel fashion. All Biomolecules listed in REMARK350 below are anti-parallel and thus are not biologically significant in nature.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fusion protein of Nociceptin receptor and cytochrome b562 / / OP4 / KOR-3 / ORL1 / NOCICEPTIN/ORPHANIN FQ RECEPTOR / Cytochrome b-562


Mass: 48077.820 Da / Num. of mol.: 2 / Mutation: M29W, H124I, K128L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo Sapiens (human)
Gene: OOR, OPRL1, ORL1, cybC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P0ABE7, UniProt: P41146

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Non-polymers , 5 types, 13 molecules

#2: Chemical ChemComp-0NN / 1-benzyl-N-[3-(1'H,3H-spiro[2-benzofuran-1,4'-piperidin]-1'-yl)propyl]-D-prolinamide


Mass: 433.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N3O2
#3: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 23

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.4
Details: 25-30% (v/v) PEG 400, 100 to 200 mM potassium sodium tartrate tetrahydrate, 100 mM BIS-TRIS propane pH 6.4 , Lipidic Cubic Phase (LCP), 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 10, 2011
Details: DOUBLE CRYSTAL MONOCHROMATOR AND K-B PAIR OF BIOMORPH MIRRORS FOR VERTICAL AND HORIZONTAL FOCUSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 16545 / Num. obs: 16545 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 58.79 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2 / % possible all: 79.5

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4DJH,1M6T

4djh

1m6t


Resolution: 3.013→32.019 Å / SU ML: 0.45 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2884 845 5.12 %random
Rwork0.2484 ---
obs0.2505 16506 93.12 %-
all-16506 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.33 Å2 / ksol: 0.307 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.6868 Å2-0 Å2-1.7825 Å2
2---12.997 Å20 Å2
3----11.4978 Å2
Refinement stepCycle: LAST / Resolution: 3.013→32.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5007 0 115 8 5130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035232
X-RAY DIFFRACTIONf_angle_d0.5637116
X-RAY DIFFRACTIONf_dihedral_angle_d13.9671859
X-RAY DIFFRACTIONf_chiral_restr0.031865
X-RAY DIFFRACTIONf_plane_restr0.004867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0134-3.2020.35091350.33092223X-RAY DIFFRACTION81
3.202-3.4490.35251170.30482595X-RAY DIFFRACTION92
3.449-3.79560.31831370.26462677X-RAY DIFFRACTION96
3.7956-4.34370.27941410.22532717X-RAY DIFFRACTION97
4.3437-5.46810.26111460.22742720X-RAY DIFFRACTION97
5.4681-32.02040.26871690.23162729X-RAY DIFFRACTION97
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)
12.62580.0068-0.2471.2587-0.44733.8211-0.1821-0.14580.32340.18630.0941-0.1699-0.2121-0.06420.06620.2690.041-0.04940.4011-0.05640.34248.8824-43.91830.0793
21.7424-2.35281.34923.2731-1.74571.0445-0.0681-0.3624-0.24750.19690.18230.3841-0.0203-0.2779-0.14110.1731-0.0132-0.12570.12280.10110.145430.5754-7.462925.1791
32.76930.11110.24031.9176-0.20734.1114-0.16340.13720.0731-0.1660.0749-0.2002-0.00830.12680.03840.209-0.01520.0050.36380.00450.235814.4296-52.244539.607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 47:331)
2X-RAY DIFFRACTION2(chain B and resseq 1003:1106)
3X-RAY DIFFRACTION3(chain B and resseq 47:333)

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