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- PDB-2lyw: Intermolecular interactions between neurotensin and the third ext... -

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Basic information

Entry
Database: PDB / ID: 2lyw
TitleIntermolecular interactions between neurotensin and the third extracellular loop of human neurotensin 1 receptor
Components
  • Neurotensin
  • Neurotensin receptor type 1
KeywordsSIGNALING PROTEIN/NEUROPEPTIDE / Interaction ligand/receptor / NTS1 / SIGNALING PROTEIN-NEUROPEPTIDE complex
Function / homology
Function and homology information


neuropeptide receptor binding / 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 ...neuropeptide receptor binding / 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 / positive regulation of inhibitory postsynaptic potential / neuropeptide hormone activity / negative regulation of systemic arterial blood pressure / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of glutamate secretion / 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 / transport vesicle / blood vessel diameter maintenance / Peptide ligand-binding receptors / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / learning / G protein-coupled receptor activity / terminal bouton / cytoplasmic side of plasma membrane / positive regulation of NF-kappaB transcription factor activity / G alpha (q) signalling events / chemical synaptic transmission / perikaryon / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / positive regulation of apoptotic process / membrane raft / G protein-coupled receptor signaling pathway / negative regulation of gene expression / intracellular membrane-bounded organelle / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / signal transduction / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / 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 / Neurotensin/neuromedin N
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsMonti, J. / Da Costa, G.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2013
Title: Intermolecular interactions between the neurotensin and the third extracellular loop of human neurotensin 1 receptor.
Authors: Da Costa, G. / Bondon, A. / Coutant, J. / Curmi, P. / Monti, J.P.
History
DepositionSep 20, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_nmr_software ...entity_poly / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotensin receptor type 1
B: Neurotensin


Theoretical massNumber of molelcules
Total (without water)4,8572
Polymers4,8572
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Neurotensin receptor type 1 / NT-R-1 / NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH


Mass: 3180.568 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 321-344 / Mutation: C327S / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P30989
#2: Protein/peptide Neurotensin / NT


Mass: 1675.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P30990

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.7 mM neurotensin, 1.4 mM hNTS1(321-344), trifluoroethanol/water
Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentSolution-ID
0.7 mMneurotensin-11
1.4 mMhNTS1(321-344)-21
Sample conditionsPressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameDeveloperClassification
Insight IIAccelrys Software Inc.simulated annealing
Insight IIAccelrys Software Inc.refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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