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- PDB-4xes: Structure of active-like neurotensin receptor -

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Basic information

Entry
Database: PDB / ID: 4xes
TitleStructure of active-like neurotensin receptor
Components
  • Neurotensin receptor type 1, Endolysin chimera
  • Neurotensin/neuromedin N
KeywordsSIGNALING PROTEIN / HYDROLASE / membrane protein / G protein-coupled receptor / GPCR / neurotensin receptor / NTSR1
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 / dendritic shaft / response to cocaine / 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 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / G-protein coupled receptors family 1 signature. ...Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / Neurotensin receptor / Neurotensin type 1 receptor / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage 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
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / 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: 2.6 Å
AuthorsKrumm, B.E. / White, J.F. / Shah, P. / Grisshammer, R.
CitationJournal: Nat Commun / Year: 2015
Title: Structural prerequisites for G-protein activation by the neurotensin receptor.
Authors: Krumm, B.E. / White, J.F. / Shah, P. / Grisshammer, R.
History
DepositionDec 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Nov 27, 2019Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurotensin receptor type 1, Endolysin chimera
B: Neurotensin/neuromedin N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,98013
Polymers61,5052
Non-polymers1,47611
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint11 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.840, 88.440, 161.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Neurotensin receptor type 1, Endolysin chimera / NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH / Lysis protein / ...NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH / Lysis protein / Lysozyme / Muramidase


Mass: 60685.809 Da / Num. of mol.: 1
Fragment: UNP residues 43-396 (P20789), residues 2-161 (P00720)
Mutation: A86L, E166A, G215A, 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 / Plasmid: pFASTBAC1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): cabbage looper / References: UniProt: P20789, UniProt: P00720, lysozyme
#2: Protein/peptide Neurotensin/neuromedin N


Mass: 819.007 Da / Num. of mol.: 1 / Fragment: UNP residues 157-162 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P20068

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Non-polymers , 5 types, 66 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 6

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 19.8-23.4% PEG400, 80 mM HEPES, 50 mM lithium citrate, 2 mM TCEP
PH range: 7.0-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→34.2 Å / Num. obs: 22591 / % possible obs: 99.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.8
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.5 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDS10 Jan 2014 Built=20140307data reduction
XSCALE4 Jul 2012, Built=20131111data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4GRV

4grv


Resolution: 2.6→34 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.883 / SU B: 28.246 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.474 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27972 1209 5.4 %RANDOM
Rwork0.22983 ---
obs0.23248 21352 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.625 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---3.39 Å20 Å2
3---3.58 Å2
Refinement stepCycle: 1 / Resolution: 2.6→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 96 55 3923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193793
X-RAY DIFFRACTIONr_bond_other_d0.0010.023639
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9655137
X-RAY DIFFRACTIONr_angle_other_deg0.76838267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2085473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14222.254142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54915567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3731525
X-RAY DIFFRACTIONr_chiral_restr0.0640.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02902
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8642.5311904
X-RAY DIFFRACTIONr_mcbond_other0.8492.5281903
X-RAY DIFFRACTIONr_mcangle_it1.4773.7892372
X-RAY DIFFRACTIONr_mcangle_other1.4843.7922373
X-RAY DIFFRACTIONr_scbond_it1.1042.7761888
X-RAY DIFFRACTIONr_scbond_other1.1032.7761888
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7734.0652765
X-RAY DIFFRACTIONr_long_range_B_refined4.31220.7564361
X-RAY DIFFRACTIONr_long_range_B_other4.31220.7724362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å
RfactorNum. reflection% reflection
Rfree0.356 89 5.6 %
Rwork0.381 1510 -
obs--98.7 %
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)
11.0278-0.60710.81582.885-1.32791.29780.10160.1525-0.01960.0105-0.06010.76410.1347-0.1263-0.04150.71650.04240.1290.34670.0340.5376-8.82532.0564-13.1266
20.339-0.84280.02343.52670.1530.03540.1033-0.1032-0.33210.09040.00220.15830.0498-0.0131-0.10560.70370.032-0.05460.57670.09010.7327.7512-24.0533-7.8499
31.0458-0.3246-0.21963.47530.75040.4542-0.18030.38370.17230.51150.0625-0.0149-0.0150.02110.11780.80020.0195-0.06580.21240.01660.36333.55210.1781-10.7872
41.35670.3781.69174.42235.28687.5022-0.32890.44860.05590.21220.4002-0.138-0.15550.9209-0.07130.6692-0.050.01870.66240.03050.634220.5926-23.0752-13.2165
52.0001-0.4202-0.10542.7941-1.15371.7761-0.15440.09930.27120.09350.1611-0.5322-0.12870.2497-0.00680.7495-0.0347-0.12740.2504-0.00470.524510.982710.2558-12.6295
60.6639-0.8051-0.08294.81451.64470.6674-0.00270.26080.12050.3350.0071-0.2248-0.00390.0735-0.00440.5912-0.00830.0090.30640.04240.3786.2679-9.6101-26.2894
70.7435-0.47080.09477.2487-2.35840.8359-0.02540.1187-0.11970.11650.18360.4280.1253-0.142-0.15820.5338-0.0194-0.03410.33120.00080.4059-3.27113.2578-21.6352
81.4079-3.0816-1.4877.74231.52924.6044-0.0390.0262-0.08180.22020.03960.1641-0.0663-0.2584-0.00050.5167-0.0611-0.04430.6383-0.02560.5563-6.0175-23.3878-14.2584
93.5355-2.5343-0.13974.5980.2820.382-0.0831-0.5532-0.52490.36120.07690.052-0.06190.23410.00620.2202-0.05080.00140.40760.1190.325815.3127-49.328-23.8539
103.91640.782-0.57723.1909-0.93253.2105-0.0286-0.01690.12620.10890.021-0.1379-0.1770.05850.00760.02060.01880.01960.099-0.01970.247916.1192-38.2474-38.5566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 90
2X-RAY DIFFRACTION2A91 - 104
3X-RAY DIFFRACTION3A105 - 171
4X-RAY DIFFRACTION4A172 - 188
5X-RAY DIFFRACTION5A189 - 250
6X-RAY DIFFRACTION6A251 - 339
7X-RAY DIFFRACTION7A340 - 371
8X-RAY DIFFRACTION8A372 - 382
9X-RAY DIFFRACTION9A383 - 1053
10X-RAY DIFFRACTION10A1054 - 1165

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