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

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Basic information

Entry
Database: PDB / ID: 4xee
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 / 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
CITRATE ANION / 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: 2.9 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 23, 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)62,5737
Polymers61,5632
Non-polymers1,0105
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-8 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.070, 88.110, 161.290
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: 60743.840 Da / Num. of mol.: 1
Fragment: UNP residues 43-396 (P20789), residues 2-161 (P00720)
Mutation: A86L, 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, 15 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 16-24% PEG400, 75 mM HEPES, pH 7.0-8.0, 1.7 mM TCEP, 32 mM lithium citrate, 0.9 mM Neurotensin (8-13)
PH range: 7.0-8.0

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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: Jul 21, 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: 2.9→46 Å / Num. obs: 14628 / % possible obs: 90.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 8.9
Reflection shellResolution: 2.9→3.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 1.5 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDS10 Jan 2014data reduction
XSCALE10 Jan 2014data scaling
PHASERVersion 2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4GRV

4grv


Resolution: 2.9→45 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.891 / SU B: 47.622 / SU ML: 0.406 / Cross valid method: THROUGHOUT / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28126 769 5.3 %RANDOM
Rwork0.23127 ---
obs0.23386 13831 90.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.923 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---3.31 Å20 Å2
3---3.12 Å2
Refinement stepCycle: 1 / Resolution: 2.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3724 0 67 10 3801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193866
X-RAY DIFFRACTIONr_bond_other_d0.0010.023792
X-RAY DIFFRACTIONr_angle_refined_deg1.0081.9635237
X-RAY DIFFRACTIONr_angle_other_deg0.72538654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1945465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.88522.342158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03815629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8131528
X-RAY DIFFRACTIONr_chiral_restr0.0560.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024240
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02932
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_it0.9183.5681874
X-RAY DIFFRACTIONr_mcbond_other0.9123.5661873
X-RAY DIFFRACTIONr_mcangle_it1.5825.3472334
X-RAY DIFFRACTIONr_mcangle_other1.5835.352335
X-RAY DIFFRACTIONr_scbond_it1.0033.8521991
X-RAY DIFFRACTIONr_scbond_other0.9913.8471989
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6775.6792902
X-RAY DIFFRACTIONr_long_range_B_refined4.59929.3494578
X-RAY DIFFRACTIONr_long_range_B_other4.629.3624579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 59 -
Rwork0.321 957 -
obs--88.5 %
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)
11.82961.5199-0.88495.81210.36811.91140.08420.0780.12530.73180.2241-1.08950.15940.1143-0.30830.67870.0407-0.25610.3034-0.0180.337630.5902-42.0912-12.628
21.9538-0.78880.21236.66380.24990.049-0.07210.3668-0.09781.47390.0487-0.07540.05720.04430.02330.97060.06880.06470.192-0.02330.131322.4201-46.8106-9.694
314.6445-6.0703-13.93049.653.252714.19930.1236-0.0290.7517-0.20430.4925-0.282-0.1334-0.2901-0.61610.51020.0314-0.09050.5988-0.04460.70455.2828-19.4573-18.0571
43.8387-0.82350.72414.16070.29681.6148-0.1331-0.1019-0.28930.2370.23011.0660.172-0.3614-0.09690.78560.02410.21320.29670.05390.348712.6402-51.0954-10.62
51.16512.4453-0.80385.3181-2.21054.366-0.22460.1552-0.2551-0.28530.3771-0.39540.14280.0036-0.15240.40670.03680.02510.23880.06680.316815.9261-24.4322-26.6537
60.8257-2.1476-0.360910.460.1580.35160.0620.1817-0.04580.2431-0.0778-0.13940.0132-0.08360.01580.4969-0.02610.02750.293-0.04620.19723.6023-48.5642-23.2288
74.41821.2498-2.4474.5196-3.54923.31740.4697-0.2441-0.5928-0.6761-0.480.29980.31140.36960.01020.7862-0.091-0.12690.8631-0.12120.85532.2865-22.0844-13.6882
87.8423-4.2634-3.90233.65134.35.58850.0578-0.54291.0043-0.24060.1857-0.391-0.23560.2146-0.24350.37830.00950.01610.2895-0.06350.150411.79134.0058-27.4235
94.69480.36321.33713.77081.02822.552-0.0815-0.50230.05770.2593-0.07990.23010.1702-0.12790.16140.12130.02720.02520.0902-0.00420.01887.3449-3.6643-35.3251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 105
2X-RAY DIFFRACTION2A106 - 165
3X-RAY DIFFRACTION3A166 - 180
4X-RAY DIFFRACTION4A181 - 244
5X-RAY DIFFRACTION5A245 - 311
6X-RAY DIFFRACTION6A312 - 371
7X-RAY DIFFRACTION7A372 - 384
8X-RAY DIFFRACTION8A1002 - 1033
9X-RAY DIFFRACTION9A1034 - 1165

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