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- PDB-6zin: Crystal structure of the neurotensin receptor 1 in complex with t... -

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Basic information

Entry
Database: PDB / ID: 6zin
TitleCrystal structure of the neurotensin receptor 1 in complex with the small molecule inverse agonist SR48692
ComponentsNeurotensin receptor type 1,DARPin,HRV 3C protease recognition sequence
KeywordsMEMBRANE PROTEIN / GPCR ligand complex / NTSR1 / SR48692 / inverse agonist
Function / homology
Function and homology information


Peptide ligand-binding receptors / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / regulation of membrane depolarization / positive regulation of arachidonate secretion / neuron spine / L-glutamate import across plasma membrane ...Peptide ligand-binding receptors / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / regulation of membrane depolarization / positive regulation of arachidonate secretion / neuron spine / L-glutamate import across plasma membrane / regulation of respiratory gaseous exchange / positive regulation of inhibitory postsynaptic potential / negative regulation of systemic arterial blood pressure / positive regulation of glutamate secretion / negative regulation of release of sequestered calcium ion into cytosol / G alpha (q) signalling events / positive regulation of inositol phosphate biosynthetic process / response to lipid / temperature homeostasis / detection of temperature stimulus involved in sensory perception of pain / neuropeptide signaling pathway / axon terminus / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / adult locomotory behavior / learning / terminal bouton / cytoplasmic side of plasma membrane / dendritic spine / perikaryon / positive regulation of apoptotic process / membrane raft / axon / neuronal cell body / dendrite / positive regulation of gene expression / protein-containing complex binding / negative regulation of apoptotic process / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Neurotensin receptor / Neurotensin type 1 receptor / 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)
Similarity search - Domain/homology
Chem-Q6Q / Neurotensin receptor type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.639 Å
AuthorsDeluigi, M. / Klipp, A. / Hilge, M. / Merklinger, L. / Klenk, C. / Plueckthun, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_182334 Switzerland
CitationJournal: Sci Adv / Year: 2021
Title: Complexes of the neurotensin receptor 1 with small-molecule ligands reveal structural determinants of full, partial, and inverse agonism.
Authors: Deluigi, M. / Klipp, A. / Klenk, C. / Merklinger, L. / Eberle, S.A. / Morstein, L. / Heine, P. / Mittl, P.R.E. / Ernst, P. / Kamenecka, T.M. / He, Y. / Vacca, S. / Egloff, P. / Honegger, A. / Pluckthun, A.
History
DepositionJun 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 17, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 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
AAA: Neurotensin receptor type 1,DARPin,HRV 3C protease recognition sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6762
Polymers53,0891
Non-polymers5871
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.980, 37.150, 91.210
Angle α, β, γ (deg.)90.000, 113.600, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Neurotensin receptor type 1,DARPin,HRV 3C protease recognition sequence / NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH


Mass: 53089.223 Da / Num. of mol.: 1
Mutation: S83G,A86L,T101R,H103D,H105Y,L119F,M121L,E124D,R143K,D150E,A161V,R167L,R213L,V234L,K235R,V240L,I253A,I260A,N262R,K263R,H305R,C332V,F342A,T354S,F358V,S362A
Source method: isolated from a genetically manipulated source
Details: Residues 61-371 represent the rat neurotensin receptor 1 mutant H4 (NTSR1-H4). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting ...Details: Residues 61-371 represent the rat neurotensin receptor 1 mutant H4 (NTSR1-H4). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting NTSR1 with the DARPin crystallisation chaperone. Residues 381 to 536 represent the DARPin crystallisation chaperone that is related to 5LW2. Residues 537 to 539 represent a short linker connecting the DARPin crystallisation chaperone with the HRV 3C protease recognition sequence. Residues 540 to 544 are part of the HRV 3C protease recognition sequence visible in the electron density.,Residues 61-371 represent the rat neurotensin receptor 1 mutant H4 (NTSR1-H4). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting NTSR1 with the DARPin crystallisation chaperone. Residues 381 to 536 represent the DARPin crystallisation chaperone that is related to 5LW2. Residues 537 to 539 represent a short linker connecting the DARPin crystallisation chaperone with the HRV 3C protease recognition sequence. Residues 540 to 544 are part of the HRV 3C protease recognition sequence visible in the electron density.,Residues 61-371 represent the rat neurotensin receptor 1 mutant H4 (NTSR1-H4). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting NTSR1 with the DARPin crystallisation chaperone. Residues 381 to 536 represent the DARPin crystallisation chaperone that is related to 5LW2. Residues 537 to 539 represent a short linker connecting the DARPin crystallisation chaperone with the HRV 3C protease recognition sequence. Residues 540 to 544 are part of the HRV 3C protease recognition sequence visible in the electron density.
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) synthetic construct (others)
Gene: Ntsr1, Ntsr / Production host: Escherichia coli (E. coli) / References: UniProt: P20789
#2: Chemical ChemComp-Q6Q / 2-[[1-(7-chloranylquinolin-4-yl)-5-(2,6-dimethoxyphenyl)pyrazol-3-yl]carbonylamino]adamantane-2-carboxylic acid


Mass: 587.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H31ClN4O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 100 mM Bis-Tris 500 mM K citrate 30% (v/v) PEG400 10 uM SR48692
PH range: 6.4-6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999879 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999879 Å / Relative weight: 1
ReflectionResolution: 2.639→28.569 Å / Num. obs: 12018 / % possible obs: 85.4 % / Redundancy: 4.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.063 / Net I/σ(I): 5.7
Reflection shellResolution: 2.639→2.965 Å / Rmerge(I) obs: 1.206 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 601 / CC1/2: 0.512 / Rpim(I) all: 0.612

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YVR

6yvr


Resolution: 2.639→28.567 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.864 / SU B: 48.599 / SU ML: 0.403 / Cross valid method: FREE R-VALUE / ESU R Free: 0.518
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3098 605 5.038 %
Rwork0.266 11403 -
all0.268 --
obs-12008 60.509 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 67.498 Å2
Baniso -1Baniso -2Baniso -3
1-1.428 Å20 Å21.514 Å2
2---2.161 Å20 Å2
3----0.427 Å2
Refinement stepCycle: LAST / Resolution: 2.639→28.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 42 0 3159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133227
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172945
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.6194445
X-RAY DIFFRACTIONr_angle_other_deg1.1231.5596680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6085437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97121.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93915402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3911511
X-RAY DIFFRACTIONr_chiral_restr0.0350.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_nbd_refined0.1750.2787
X-RAY DIFFRACTIONr_symmetry_nbd_other0.160.22645
X-RAY DIFFRACTIONr_nbtor_refined0.1510.21618
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.264
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1030.23
X-RAY DIFFRACTIONr_nbd_other0.120.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0950.21
X-RAY DIFFRACTIONr_mcbond_it0.756.2571762
X-RAY DIFFRACTIONr_mcbond_other0.756.261763
X-RAY DIFFRACTIONr_mcangle_it1.3419.3782194
X-RAY DIFFRACTIONr_mcangle_other1.3419.3782194
X-RAY DIFFRACTIONr_scbond_it0.66.3641465
X-RAY DIFFRACTIONr_scbond_other0.66.3671466
X-RAY DIFFRACTIONr_scangle_it1.1069.5442251
X-RAY DIFFRACTIONr_scangle_other1.1069.5482252
X-RAY DIFFRACTIONr_lrange_it5.305118.85413482
X-RAY DIFFRACTIONr_lrange_other5.305118.85713483
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc work% reflection obs (%)WRfactor RworkFsc free
2.639-2.70700.627220.62714220.3881.54710.557
2.707-2.780.29460.39830.38413930.4886.38910.4230.431
2.78-2.860.4100.351600.35313980.53912.16020.3610.469
2.86-2.9470.608110.362460.36912820.60620.04680.3670.472
2.947-3.0430.398140.3363610.33812890.65929.09230.3450.507
3.043-3.1480.391180.3334500.33512660.71736.96680.340.526
3.148-3.2650.354320.3375610.33811880.72749.91580.3270.723
3.265-3.3970.339370.3097960.3111800.75270.59320.3030.749
3.397-3.5460.263520.3129500.30910880.78192.09560.2960.809
3.546-3.7160.361630.29610130.310970.82998.08570.290.804
3.716-3.9130.322500.2679350.2699940.88499.09460.2540.855
3.913-4.1460.289480.2489440.2510000.90699.20.2390.886
4.146-4.4250.235300.248460.248830.92899.20720.2320.932
4.425-4.770.274380.2348170.2368640.93398.95830.2360.924
4.77-5.2110.302430.2437420.2467950.92598.74210.250.881
5.211-5.8020.494360.316710.3187200.86298.19440.3110.824
5.802-6.6540.432450.3485960.3546490.84998.76730.3650.799
6.654-8.0410.257350.2385010.245560.9396.40290.2660.905
8.041-10.9470.165160.1884400.1884620.96398.70130.2230.976
10.947-28.5690.29210.2992690.2982980.91497.31540.3210.924
Refinement TLS params.Method: refined / Origin x: -14.0894 Å / Origin y: 4.5328 Å / Origin z: 18.3224 Å
111213212223313233
T0.076 Å2-0.0585 Å2-0.0141 Å2-0.201 Å2-0.0333 Å2--0.0395 Å2
L0.9671 °20.2741 °20.9284 °2-0.4873 °20.0948 °2--1.1124 °2
S-0.1623 Å °0.1606 Å °0.0771 Å °-0.134 Å °0.1108 Å °-0.0479 Å °-0.1068 Å °0.2715 Å °0.0515 Å °
Refinement TLS groupSelection: ALL

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