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- PDB-4grv: The crystal structure of the neurotensin receptor NTS1 in complex... -

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Basic information

Entry
Database: PDB / ID: 4grv
TitleThe crystal structure of the neurotensin receptor NTS1 in complex with neurotensin (8-13)
Components
  • Neurotensin 8-13
  • Neurotensin receptor type 1, lysozyme chimera
KeywordsSIGNALING PROTEIN/AGONIST / G-protein coupled receptor / neurotensin receptor / G-protein / SIGNALING PROTEIN-AGONIST complex
Function / homology
Function and homology information


response to antipsychotic drug / Peptide ligand-binding receptors / neuropeptide receptor binding / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / positive regulation of inhibitory postsynaptic potential / symmetric synapse / response to mineralocorticoid / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion ...response to antipsychotic drug / Peptide ligand-binding receptors / neuropeptide receptor binding / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / positive regulation of inhibitory postsynaptic potential / symmetric synapse / response to mineralocorticoid / 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 / neuropeptide hormone activity / digestive tract development / negative regulation of systemic arterial blood pressure / hyperosmotic response / negative regulation of release of sequestered calcium ion into cytosol / G alpha (q) signalling events / positive regulation of glutamate secretion / positive regulation of inositol phosphate biosynthetic process / temperature homeostasis / response to corticosterone / response to lipid / regulation of membrane depolarization / cellular response to lithium ion / detection of temperature stimulus involved in sensory perception of pain / neuropeptide signaling pathway / response to axon injury / axon terminus / transport vesicle / viral release from host cell by cytolysis / response to amphetamine / blood vessel diameter maintenance / cellular response to dexamethasone stimulus / adult locomotory behavior / peptidoglycan catabolic process / cellular response to nerve growth factor stimulus / positive regulation of release of sequestered calcium ion into cytosol / response to cocaine / dendritic shaft / liver development / learning / visual learning / terminal bouton / cytoplasmic side of plasma membrane / cell wall macromolecule catabolic process / response to estradiol / lysozyme / lysozyme activity / perikaryon / host cell cytoplasm / dendritic spine / receptor ligand activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to bacterium / positive regulation of apoptotic process / membrane raft / axon / negative regulation of gene expression / dendrite / neuronal cell body / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / cell surface / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / Neurotensin receptor / Neurotensin type 1 receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 ...Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / Neurotensin receptor / Neurotensin type 1 receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / 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) / Lysozyme-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Endolysin / Neurotensin/neuromedin N / Neurotensin receptor type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsNoinaj, N. / White, J.F. / Shibata, Y. / Love, J. / Kloss, B. / Xu, F. / Gvozdenovic-Jeremic, J. / Shah, P. / Shiloach, J. / Tate, C.G. / Grisshammer, R.
CitationJournal: Nature / Year: 2012
Title: Structure of the agonist-bound neurotensin receptor.
Authors: White, J.F. / Noinaj, N. / Shibata, Y. / Love, J. / Kloss, B. / Xu, F. / Gvozdenovic-Jeremic, J. / Shah, P. / Shiloach, J. / Tate, C.G. / Grisshammer, R.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 7, 2012Group: Database references
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999CHAIN A IS AN INTERNAL FUSION OF LYSOZYME (RESIDUES 2-161 OF UNP P00720) BETWEEN RESIDUES 52-268 ...CHAIN A IS AN INTERNAL FUSION OF LYSOZYME (RESIDUES 2-161 OF UNP P00720) BETWEEN RESIDUES 52-268 AND RESIDUES 300-379 OF Neurotensin receptor type 1 (UNP P20789). AN OFFSET OF 1000 HAS BEEN ADDED TO LYSOZYME RESIDUE NUMBERS WITHIN THE COORDINATES TO DISTINGUISH THAT PORTION OF CHAIN A. LYSOZYME RESIDUES ARE THEREFORE NUMBERED 1002-1161.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotensin receptor type 1, lysozyme chimera
B: Neurotensin 8-13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4984
Polymers58,0212
Non-polymers4772
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-7 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.960, 69.619, 97.550
Angle α, β, γ (deg.)90.00, 101.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 57201.965 Da / Num. of mol.: 1 / Fragment: see remark 999 / Mutation: A86L, E166A, G215A, L310A, F358A, V360A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: Ntsr1, Ntsr, E / Plasmid: pFastBac1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P20789, UniProt: P00720
#2: Protein/peptide Neurotensin 8-13


Mass: 819.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P20068*PLUS
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 7.4
Details: 80 mM HEPES pH 7.0, 2 mM TCEP, 43 mM NaK tartrate, 20.8% PEG400, Lipid cubic phase (LCP), temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 1, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. all: 16317 / Num. obs: 14956 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.65 / % possible all: 86.4

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASER(PHENIX)phasing
PHENIX(phenix.refine: dev_1042)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NY9

3ny9


Resolution: 2.802→14.958 Å / SU ML: 0.56 / σ(F): 0 / Phase error: 34.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2818 763 5.12 %random
Rwork0.2254 ---
obs0.2284 14895 --
all-16317 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.802→14.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 30 23 3546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053602
X-RAY DIFFRACTIONf_angle_d1.0144921
X-RAY DIFFRACTIONf_dihedral_angle_d16.2211221
X-RAY DIFFRACTIONf_chiral_restr0.073591
X-RAY DIFFRACTIONf_plane_restr0.004605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.802-3.01650.38991570.35432485X-RAY DIFFRACTION83
3.0165-3.31710.4071510.30182762X-RAY DIFFRACTION90
3.3171-3.79030.33191400.26062864X-RAY DIFFRACTION94
3.7903-4.74980.26721640.19622968X-RAY DIFFRACTION97
4.7498-14.95790.21081510.18053053X-RAY DIFFRACTION97
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)
10.7873-0.06560.97752.2391-1.16051.5953-0.06890.0684-0.0707-0.0429-0.0986-0.10940.07270.30360.17570.67650.01670.12160.5944-0.00670.501893.2333-14.067147.9021
23.31181.27421.39282.35050.022.148-0.1933-0.1501-0.4726-0.1550.2773-0.27520.3720.17880.04450.7330.15190.13790.50290.0760.638783.9221-9.703751.6099
33.8523-1.618-1.05167.74431.90915.4230.09230.2188-0.05710.21120.060.31750.0512-0.3552-0.26330.651-0.09590.14650.50590.04180.621168.0939-1.54147
42.01570.5601-4.07262.00351.99942.0081-0.2402-1.581-0.379-0.2753-0.4613-0.9826-1.5535-0.5750.49491.3877-0.0128-0.03651.05520.08750.517890.4572-11.761270.2388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 301 )
2X-RAY DIFFRACTION2chain 'A' and (resid 302 through 373 )
3X-RAY DIFFRACTION3chain 'A' and (resid 374 through 1165 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 13 )

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