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- PDB-6z66: Crystal structure of apo-state neurotensin receptor 1 -

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Basic information

Entry
Database: PDB / ID: 6z66
TitleCrystal structure of apo-state neurotensin receptor 1
ComponentsNeurotensin receptor type 1,Neurotensin receptor type 1,DARPin
KeywordsMEMBRANE PROTEIN / GPCR / apo-state / rNTSR1
Function / homology
Function and homology information


Peptide ligand-binding receptors / positive regulation of locomotion / G protein-coupled neurotensin receptor activity / regulation of inositol trisphosphate biosynthetic process / 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 ...Peptide ligand-binding receptors / positive regulation of locomotion / G protein-coupled neurotensin receptor activity / regulation of inositol trisphosphate biosynthetic process / 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 / vocalization behavior / neuron spine / L-glutamate import across plasma membrane / regulation of behavioral fear response / regulation of respiratory gaseous exchange / cAMP biosynthetic process / positive regulation of inhibitory postsynaptic potential / negative regulation of systemic arterial blood pressure / negative regulation of release of sequestered calcium ion into cytosol / G alpha (q) signalling events / positive regulation of glutamate secretion / response to food / temperature homeostasis / response to lipid / positive regulation of inositol phosphate biosynthetic process / detection of temperature stimulus involved in sensory perception of pain / response to stress / associative learning / conditioned place preference / neuropeptide signaling pathway / axon terminus / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / adult locomotory behavior / learning / cytoplasmic side of plasma membrane / terminal bouton / perikaryon / dendritic spine / positive regulation of apoptotic process / membrane raft / axon / neuronal cell body / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / 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
Neurotensin receptor type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.192 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
DepositionMay 27, 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 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Neurotensin receptor type 1,Neurotensin receptor type 1,DARPin


Theoretical massNumber of molelcules
Total (without water)53,0891
Polymers53,0891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.186, 212.992, 94.639
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Neurotensin receptor type 1,Neurotensin receptor type 1,DARPin / 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 58-371 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 58-371 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
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: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 293.1 K / Method: lipidic cubic phase / pH: 4.5
Details: 100 mM Na acetate 400-475 mM K citrate 30-31% (v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000031 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 3.192→29.461 Å / Num. obs: 10818 / % possible obs: 91.6 % / Redundancy: 13.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.094 / Rrim(I) all: 0.344 / Net I/σ(I): 7.7
Reflection shellResolution: 3.192→3.435 Å / Rmerge(I) obs: 3.661 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 541 / CC1/2: 0.316 / Rpim(I) all: 1.034 / Rrim(I) all: 3.807

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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: 3.192→29.461 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.876 / WRfactor Rfree: 0.278 / WRfactor Rwork: 0.275 / SU B: 31.612 / SU ML: 0.493 / Average fsc free: 0.8453 / Average fsc work: 0.8511 / Cross valid method: FREE R-VALUE / ESU R Free: 0.573
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2943 524 4.844 %
Rwork0.2859 10294 -
all0.286 --
obs-10818 81.948 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.754 Å2
Baniso -1Baniso -2Baniso -3
1-1.044 Å20 Å20 Å2
2---1.089 Å20 Å2
3---0.045 Å2
Refinement stepCycle: LAST / Resolution: 3.192→29.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3241 0 0 0 3241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133314
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172938
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.6174567
X-RAY DIFFRACTIONr_angle_other_deg1.1321.5586673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1275456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43923.036112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71315393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.777156
X-RAY DIFFRACTIONr_chiral_restr0.0350.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02701
X-RAY DIFFRACTIONr_nbd_refined0.1820.2799
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.22520
X-RAY DIFFRACTIONr_nbtor_refined0.1510.21654
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21460
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.284
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2620.27
X-RAY DIFFRACTIONr_nbd_other0.1660.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3010.22
X-RAY DIFFRACTIONr_mcbond_it1.2427.2721833
X-RAY DIFFRACTIONr_mcbond_other1.2417.271832
X-RAY DIFFRACTIONr_mcangle_it2.23110.9032286
X-RAY DIFFRACTIONr_mcangle_other2.23110.9042287
X-RAY DIFFRACTIONr_scbond_it0.967.2441481
X-RAY DIFFRACTIONr_scbond_other0.967.2461482
X-RAY DIFFRACTIONr_scangle_it1.75410.8482281
X-RAY DIFFRACTIONr_scangle_other1.75410.8492282
X-RAY DIFFRACTIONr_lrange_it6.238135.22213665
X-RAY DIFFRACTIONr_lrange_other6.238135.21713666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.192-3.27400.43523X-RAY DIFFRACTION2.416
3.274-3.3640.452120.391205X-RAY DIFFRACTION23.2334
3.364-3.4620.36290.346406X-RAY DIFFRACTION48.1195
3.462-3.5680.37280.331649X-RAY DIFFRACTION76.8445
3.568-3.6850.348370.345794X-RAY DIFFRACTION96.0694
3.685-3.8140.271500.316778X-RAY DIFFRACTION99.3998
3.814-3.9580.323400.284762X-RAY DIFFRACTION100
3.958-4.1190.289350.29729X-RAY DIFFRACTION100
4.119-4.3020.238260.268730X-RAY DIFFRACTION100
4.302-4.5120.313320.242677X-RAY DIFFRACTION100
4.512-4.7550.295390.251647X-RAY DIFFRACTION100
4.755-5.0430.279360.257604X-RAY DIFFRACTION100
5.043-5.390.269290.264586X-RAY DIFFRACTION100
5.39-5.8210.364270.36538X-RAY DIFFRACTION100
5.821-6.3750.322230.386511X-RAY DIFFRACTION100
6.375-7.1240.315170.378462X-RAY DIFFRACTION99.7917
7.124-8.220.227230.26410X-RAY DIFFRACTION100
8.22-10.0520.241170.203349X-RAY DIFFRACTION100
10.052-14.1530.302110.225284X-RAY DIFFRACTION100
14.153-29.4610.266130.345150X-RAY DIFFRACTION87.1658

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