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Yorodumi- PDB-6z8n: Crystal structure of the neurotensin receptor 1 in complex with t... -
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-Basic information
Entry | Database: PDB / ID: 6z8n | ||||||
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Title | Crystal structure of the neurotensin receptor 1 in complex with the small-molecule full agonist SRI-9829 | ||||||
Components | Neurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor type 1,Neurotensin receptor 1 (NTSR1),Neurotensin receptor 1 (NTSR1) | ||||||
Keywords | MEMBRANE PROTEIN / GPCR-ligand complex / rNTSR1 / SRI-9829 / full 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 / positive regulation of inhibitory postsynaptic potential / regulation of membrane depolarization / positive regulation of arachidonate secretion / 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 / positive regulation of inhibitory postsynaptic potential / regulation of membrane depolarization / positive regulation of arachidonate secretion / L-glutamate import across plasma membrane / neuron spine / regulation of respiratory gaseous exchange / positive regulation of glutamate secretion / 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 inositol phosphate biosynthetic process / temperature homeostasis / response to lipid / 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 / learning / dendritic shaft / 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 | ||||||
Biological species | Rattus norvegicus (Norway rat) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å | ||||||
Authors | Deluigi, M. / Klipp, A. / Hilge, M. / Merklinger, L. / Klenk, C. / Plueckthun, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z8n.cif.gz | 176.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z8n.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6z8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z8n_validation.pdf.gz | 790.3 KB | Display | wwPDB validaton report |
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Full document | 6z8n_full_validation.pdf.gz | 791.9 KB | Display | |
Data in XML | 6z8n_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 6z8n_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/6z8n ftp://data.pdbj.org/pub/pdb/validation_reports/z8/6z8n | HTTPS FTP |
-Related structure data
Related structure data | 6yvrSC 6z4qC 6z4sC 6z4vC 6z66C 6za8C 6zinC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 60-371 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 60-371 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 60-371 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 |
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#2: Chemical | ChemComp-SR9 / ( |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.92 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase / pH: 6.8 Details: 100 mM HEPES 370-520 mM Na citrate 32% (v/v) PEG400 10 uM SRI-9829 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999998 Å / Relative weight: 1 |
Reflection | Resolution: 2.803→29.595 Å / Num. obs: 13189 / % possible obs: 90.4 % / Redundancy: 5.2 % / CC1/2: 0.982 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.099 / Rrim(I) all: 0.232 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.803→3.127 Å / Rmerge(I) obs: 1.866 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 660 / CC1/2: 0.32 / Rpim(I) all: 0.82 / Rrim(I) all: 2.05 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YVR Resolution: 2.803→29.595 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.307 / WRfactor Rwork: 0.296 / SU B: 19.62 / SU ML: 0.364 / Average fsc free: 0.8412 / Average fsc work: 0.8649 / Cross valid method: FREE R-VALUE / ESU R Free: 0.501 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.825 Å2
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Refinement step | Cycle: LAST / Resolution: 2.803→29.595 Å
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Refine LS restraints |
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LS refinement shell |
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