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- PDB-6z4s: Crystal structure of the neurotensin receptor 1 (NTSR1-H4bmx) in ... -

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Basic information

Entry
Database: PDB / ID: 6z4s
TitleCrystal structure of the neurotensin receptor 1 (NTSR1-H4bmx) 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 / positive regulation of inhibitory postsynaptic potential / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / L-glutamate import across plasma membrane / positive regulation of arachidonic acid secretion / neuron spine ...Peptide ligand-binding receptors / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / positive regulation of inhibitory postsynaptic potential / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / L-glutamate import across plasma membrane / positive regulation of arachidonic acid secretion / neuron spine / regulation of respiratory gaseous exchange / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of systemic arterial blood pressure / G alpha (q) signalling events / positive regulation of glutamate secretion / positive regulation of inositol phosphate biosynthetic process / temperature homeostasis / response to lipid / regulation of membrane depolarization / detection of temperature stimulus involved in sensory perception of pain / neuropeptide signaling pathway / axon terminus / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / learning / terminal bouton / cytoplasmic side of plasma membrane / perikaryon / dendritic spine / positive regulation of apoptotic process / membrane raft / axon / neuronal cell body / dendrite / protein-containing complex binding / positive regulation of gene expression / 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: 2.707 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 25, 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

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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)53,7402
Polymers53,1531
Non-polymers5871
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.518, 77.727, 158.394
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 53153.266 Da / Num. of mol.: 1
Mutation: S83G,A86L,T101R,H103D,H105Y,L119F,M121L,R143K,A161V,R167L,R213L,V234L,K235R,V240L,I253A,I260A,N262R,K263R,H305R,C332V,F342A,T354S
Source method: isolated from a genetically manipulated source
Details: Residues 60-371 represent the rat neurotensin receptor 1 mutant H4bm (NTSR1-H4bm). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting ...Details: Residues 60-371 represent the rat neurotensin receptor 1 mutant H4bm (NTSR1-H4bm). 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 545 are part of the HRV 3C protease recognition sequence visible in the electron density.,Residues 60-371 represent the rat neurotensin receptor 1 mutant H4bm (NTSR1-H4bm). 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 545 are part of the HRV 3C protease recognition sequence visible in the electron density.,Residues 60-371 represent the rat neurotensin receptor 1 mutant H4bm (NTSR1-H4bm). 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 545 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

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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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 100 mM Na citrate 225-460 mM ammonium nitrate 30-32% (v/v) PEG400 1 uM SR48692
PH range: 4.8-51

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000009 Å / Relative weight: 1
ReflectionResolution: 2.707→29.353 Å / Num. obs: 10475 / % possible obs: 90.6 % / Redundancy: 7.3 % / CC1/2: 0.964 / Rmerge(I) obs: 0.525 / Rpim(I) all: 0.198 / Rrim(I) all: 0.564 / Net I/σ(I): 4.3
Reflection shellResolution: 2.707→3.029 Å / Rmerge(I) obs: 4.678 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 524 / CC1/2: 0.294 / Rpim(I) all: 1.504 / Rrim(I) all: 4.929
Serial crystallography sample deliveryMethod: fixed target

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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: 2.707→29.353 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.848 / WRfactor Rfree: 0.285 / WRfactor Rwork: 0.269 / SU B: 21.592 / SU ML: 0.412 / Average fsc free: 0.8505 / Average fsc work: 0.8675 / Cross valid method: FREE R-VALUE / ESU R Free: 0.523
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2889 552 5.27 %
Rwork0.2727 9922 -
all0.274 --
obs-10474 68.408 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.575 Å2
Baniso -1Baniso -2Baniso -3
1-0.315 Å20 Å20 Å2
2--1.193 Å20 Å2
3----1.508 Å2
Refinement stepCycle: LAST / Resolution: 2.707→29.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 42 0 3330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0133406
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173099
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.6144678
X-RAY DIFFRACTIONr_angle_other_deg1.081.5747077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8685444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94822.932133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32415460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.631510
X-RAY DIFFRACTIONr_chiral_restr0.0320.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02719
X-RAY DIFFRACTIONr_nbd_refined0.1670.2764
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1450.22806
X-RAY DIFFRACTIONr_nbtor_refined0.1520.21694
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21680
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1260.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1170.217
X-RAY DIFFRACTIONr_nbd_other0.1350.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0910.22
X-RAY DIFFRACTIONr_mcbond_it0.5234.371790
X-RAY DIFFRACTIONr_mcbond_other0.5234.3711791
X-RAY DIFFRACTIONr_mcangle_it0.9766.5472229
X-RAY DIFFRACTIONr_mcangle_other0.9766.5472229
X-RAY DIFFRACTIONr_scbond_it0.2844.431616
X-RAY DIFFRACTIONr_scbond_other0.2844.431617
X-RAY DIFFRACTIONr_scangle_it0.5726.6322449
X-RAY DIFFRACTIONr_scangle_other0.5726.6332450
X-RAY DIFFRACTIONr_lrange_it3.38782.32714162
X-RAY DIFFRACTIONr_lrange_other3.38982.30614148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.707-2.7770.23520.33831X-RAY DIFFRACTION3.0165
2.777-2.8530.71450.33671X-RAY DIFFRACTION7.1028
2.853-2.9360.15550.397110X-RAY DIFFRACTION10.8083
2.936-3.0260.522150.375260X-RAY DIFFRACTION27.5
3.026-3.1250.327200.356477X-RAY DIFFRACTION49.2079
3.125-3.2340.337330.323572X-RAY DIFFRACTION63.4172
3.234-3.3560.345410.323694X-RAY DIFFRACTION77.2871
3.356-3.4930.317520.299810X-RAY DIFFRACTION99.3088
3.493-3.6480.262430.272839X-RAY DIFFRACTION100
3.648-3.8260.215340.274776X-RAY DIFFRACTION100
3.826-4.0320.31380.242770X-RAY DIFFRACTION100
4.032-4.2760.224380.246708X-RAY DIFFRACTION100
4.276-4.570.307350.235667X-RAY DIFFRACTION99.8577
4.57-4.9350.316300.235641X-RAY DIFFRACTION99.7028
4.935-5.4040.249320.288574X-RAY DIFFRACTION100
5.404-6.0380.304410.337525X-RAY DIFFRACTION100
6.038-6.9660.31250.308478X-RAY DIFFRACTION99.8016
6.966-8.5150.316390.241396X-RAY DIFFRACTION99.5423
8.515-11.9730.203160.205324X-RAY DIFFRACTION99.7067
11.973-29.3530.32980.329199X-RAY DIFFRACTION92.4107

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