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

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Basic information

Entry
Database: PDB / ID: 6yvr
TitleCrystal structure of the neurotensin receptor 1 in complex with the peptide full agonist NTS8-13
Components
  • Neurotensin receptor type 1,Neurotensin receptor type 1,DARPin crystallisation chaperone
  • neurotensin NTS8-13 (full agonist)
KeywordsMEMBRANE PROTEIN / GPCR-ligand complex / NTSR1 / NTS8-13 / full agonist
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 / positive regulation of inositol phosphate biosynthetic process / response to lipid / response to stress / detection of temperature stimulus involved in sensory perception of pain / 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: 2.458 Å
AuthorsDeluigi, M. / Merklinger, L. / Hilge, M. / Ernst, P. / Klipp, A. / 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
DepositionApr 28, 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 1.2Jan 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 1.3Nov 13, 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

Downloads & links

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Assembly

Deposited unit
AAA: Neurotensin receptor type 1,Neurotensin receptor type 1,DARPin crystallisation chaperone
BBB: Neurotensin receptor type 1,Neurotensin receptor type 1,DARPin crystallisation chaperone
CCC: neurotensin NTS8-13 (full agonist)
DDD: neurotensin NTS8-13 (full agonist)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,49612
Polymers108,0454
Non-polymers2,4518
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11930 Å2
ΔGint-36 kcal/mol
Surface area39890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.886, 114.001, 195.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

#1: Protein Neurotensin receptor type 1,Neurotensin receptor type 1,DARPin crystallisation chaperone / NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH


Mass: 53089.223 Da / Num. of mol.: 2
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 50-371 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- ...Details: residues 50-371 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-H4 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 543 are part of the HRV 3C protease recognition sequence visible in the electron density,residues 50-371 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-H4 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 543 are part of the HRV 3C protease recognition sequence visible in the electron density,residues 50-371 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-H4 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 543 are part of the HRV 3C protease recognition sequence visible in the electron density,residues 50-371 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-H4 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 543 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: Protein/peptide neurotensin NTS8-13 (full agonist)


Mass: 933.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RRPYIL represent the six C-terminal residues of the endogenous full agonist
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli)
#3: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.49 Å3/Da / Density % sol: 72.58 %
Crystal growTemperature: 277.1 K / Method: vapor diffusion, sitting drop / pH: 9.4
Details: 50mM glycine 1M NaCl 8.3% (w/v) PEG4000 Cryoprotectant solution contained: 50mM glycine pH 9.4 1M NaCl 100nM NTS8-13 15% (v/v) PEG600 15% (v/v) glycerol

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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: Jun 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.458→29.633 Å / Num. obs: 59974 / % possible obs: 93.9 % / Redundancy: 12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.028 / Rrim(I) all: 0.098 / Net I/σ(I): 15.2
Reflection shellResolution: 2.458→2.647 Å / Rmerge(I) obs: 1.711 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3000 / CC1/2: 0.597 / Rpim(I) all: 0.555 / Rrim(I) all: 1.801

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XEE

4xee


Resolution: 2.458→29.633 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.217 / SU B: 17.003 / SU ML: 0.172 / Average fsc free: 0.9104 / Average fsc work: 0.9137 / Cross valid method: FREE R-VALUE / ESU R: 0.316 / ESU R Free: 0.228
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2375 2958 4.932 %
Rwork0.2284 57016 -
all0.229 --
obs-59974 81.168 %
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: 70.765 Å2
Baniso -1Baniso -2Baniso -3
1--0.652 Å20 Å20 Å2
2---0.561 Å20 Å2
3---1.213 Å2
Refinement stepCycle: LAST / Resolution: 2.458→29.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7134 0 168 48 7350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0137464
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176956
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.65110197
X-RAY DIFFRACTIONr_angle_other_deg1.1931.61315952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3455950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93121.603312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.168151041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6941536
X-RAY DIFFRACTIONr_chiral_restr0.0540.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021590
X-RAY DIFFRACTIONr_nbd_refined0.1890.21572
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.26077
X-RAY DIFFRACTIONr_nbtor_refined0.1540.23661
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2149
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0890.29
X-RAY DIFFRACTIONr_nbd_other0.1540.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.25
X-RAY DIFFRACTIONr_mcbond_it3.5184.8263818
X-RAY DIFFRACTIONr_mcbond_other3.5174.8263817
X-RAY DIFFRACTIONr_mcangle_it5.0257.2494762
X-RAY DIFFRACTIONr_mcangle_other5.0257.2494763
X-RAY DIFFRACTIONr_scbond_it4.4655.23646
X-RAY DIFFRACTIONr_scbond_other4.4655.23646
X-RAY DIFFRACTIONr_scangle_it6.427.6545435
X-RAY DIFFRACTIONr_scangle_other6.427.6545435
X-RAY DIFFRACTIONr_lrange_it7.73658.7098137
X-RAY DIFFRACTIONr_lrange_other7.73658.7128138
X-RAY DIFFRACTIONr_ncsr_local_group_10.0340.0514813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.458-2.5210.313150.328359X-RAY DIFFRACTION6.9323
2.521-2.590.28370.3031023X-RAY DIFFRACTION20.0113
2.59-2.6650.2981100.2872153X-RAY DIFFRACTION44.5999
2.665-2.7470.3131820.2983520X-RAY DIFFRACTION74.2628
2.747-2.8370.3032250.2764183X-RAY DIFFRACTION91.6234
2.837-2.9370.2542480.2534333X-RAY DIFFRACTION98.368
2.937-3.0480.252190.2254293X-RAY DIFFRACTION100
3.048-3.1720.2442080.2184156X-RAY DIFFRACTION100
3.172-3.3130.2352030.2123980X-RAY DIFFRACTION99.9522
3.313-3.4740.2381930.2133804X-RAY DIFFRACTION100
3.474-3.6620.2211610.1973636X-RAY DIFFRACTION99.9737
3.662-3.8840.2141730.2043429X-RAY DIFFRACTION99.9445
3.884-4.1520.2251680.2083263X-RAY DIFFRACTION99.9709
4.152-4.4840.1841590.23008X-RAY DIFFRACTION99.9369
4.484-4.9110.2031470.1932787X-RAY DIFFRACTION99.9659
4.911-5.4880.2221380.2342536X-RAY DIFFRACTION99.9626
5.488-6.3340.2971100.2932275X-RAY DIFFRACTION99.8744
6.334-7.750.2541200.2431905X-RAY DIFFRACTION100
7.75-10.9260.203920.1751512X-RAY DIFFRACTION100
10.926-29.6330.365500.387861X-RAY DIFFRACTION94.4041
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)
10.73930.22540.05811.92350.21411.5723-0.04760.2809-0.0564-0.57470.081-0.2327-0.04360.2447-0.03350.2083-0.04570.06220.214-0.00120.035216.1214-25.6457-43.322
20.81970.16070.26121.6179-0.36061.5837-0.01790.20950.0396-0.50280.0960.466-0.0037-0.303-0.07810.2237-0.0272-0.13050.21850.01710.1425-14.1224-27.5446-39.1879
37.01097.4358-8.06497.9139-8.57329.4012-0.4255-0.2984-0.8715-0.3823-0.4001-0.92930.58120.4850.82550.51690.0941-0.24550.5393-0.15210.42530.6653-33.6395-20.1436
47.7451.5336-1.99334.55773.284312.62680.206-0.01890.7859-0.3887-0.13310.662-0.8176-0.287-0.07290.17340.02170.02520.26820.03720.1758-21.9888-19.4831-12.9718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA50 - 543
2X-RAY DIFFRACTION2ALLBBB50 - 543
3X-RAY DIFFRACTION3ALLCCC1006 - 1013
4X-RAY DIFFRACTION4ALLDDD1006 - 1013

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