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- PDB-6z4v: Crystal structure of the neurotensin receptor 1 (NTSR1-H4bmx) in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6z4v | ||||||
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Title | Crystal structure of the neurotensin receptor 1 (NTSR1-H4bmx) in complex with NTS8-13 | ||||||
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![]() | MEMBRANE PROTEIN / GPCR-ligand complex / rNTSR1 / NTS8-13 / full agonist | ||||||
Function / homology | ![]() 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 / L-glutamate import across plasma membrane / positive regulation of arachidonic acid secretion / regulation of respiratory gaseous exchange ...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 / L-glutamate import across plasma membrane / positive regulation of arachidonic acid secretion / regulation of respiratory gaseous exchange / neuron spine / positive regulation of inhibitory postsynaptic potential / negative regulation of systemic arterial blood pressure / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of glutamate secretion / 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 / 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 | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deluigi, M. / Klipp, A. / Hilge, M. / Merklinger, L. / Klenk, C. / Plueckthun, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.4 KB | Display | ![]() |
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Full document | ![]() | 443.8 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yvrSC ![]() 6z4qC ![]() 6z4sC ![]() 6z66C ![]() 6z8nC ![]() 6za8C ![]() 6zinC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | 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 52-371 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 52-371 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.) ![]() ![]() Gene: Ntsr1, Ntsr / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 819.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.19 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase Details: 100 mM MES 350-450 mM ammonium tartrate 30% (v/v) PEG400 10 uM NTS8-13 PH range: 6.2-6.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000009 Å / Relative weight: 1 |
Reflection | Resolution: 2.595→29.251 Å / Num. obs: 14177 / % possible obs: 88.9 % / Redundancy: 8.5 % / CC1/2: 0.921 / Rmerge(I) obs: 0.453 / Rpim(I) all: 0.165 / Rrim(I) all: 0.484 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.595→2.802 Å / Rmerge(I) obs: 2.576 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 709 / CC1/2: 0.458 / Rpim(I) all: 0.97 / Rrim(I) all: 2.76 |
Serial crystallography sample delivery | Method: fixed target |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6YVR Resolution: 2.595→29.251 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.863 / SU B: 17.265 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / ESU R Free: 0.39 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: 33.074 Å2
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Refinement step | Cycle: LAST / Resolution: 2.595→29.251 Å
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Refine LS restraints |
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LS refinement shell |
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