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- PDB-4bwb: Structure of Evolved Agonist-bound Neurotensin Receptor 1 Mutant ... -

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Basic information

Entry
Database: PDB / ID: 4bwb
TitleStructure of Evolved Agonist-bound Neurotensin Receptor 1 Mutant without Lysozyme Fusion
Components
  • NEUROTENSIN
  • NEUROTENSIN RECEPTOR TYPE 1
KeywordsSIGNALING PROTEIN / G PROTEIN COUPLED RECEPTOR / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of locomotion involved in locomotory behavior / Peptide ligand-binding receptors / positive regulation of locomotion / neuropeptide receptor binding / G protein-coupled neurotensin receptor activity / regulation of inositol trisphosphate biosynthetic process / inositol phosphate catabolic process / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion ...regulation of locomotion involved in locomotory behavior / Peptide ligand-binding receptors / positive regulation of locomotion / neuropeptide receptor binding / G protein-coupled neurotensin receptor activity / regulation of inositol trisphosphate biosynthetic process / inositol phosphate catabolic process / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / regulation of membrane depolarization / positive regulation of arachidonate secretion / vocalization behavior / response to antipsychotic drug / neuron spine / L-glutamate import across plasma membrane / regulation of behavioral fear response / regulation of respiratory gaseous exchange / neuropeptide hormone activity / cAMP biosynthetic process / positive regulation of inhibitory postsynaptic potential / negative regulation of systemic arterial blood pressure / negative regulation of release of sequestered calcium ion into cytosol / digestive tract development / G alpha (q) signalling events / positive regulation of glutamate secretion / hyperosmotic response / response to mineralocorticoid / response to food / response to corticosterone / cellular response to lithium ion / temperature homeostasis / response to lipid / positive regulation of inositol phosphate biosynthetic process / detection of temperature stimulus involved in sensory perception of pain / response to stress / associative learning / conditioned place preference / cellular response to dexamethasone stimulus / neuropeptide signaling pathway / response to axon injury / transport vesicle / axon terminus / response to amphetamine / blood vessel diameter maintenance / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / adult locomotory behavior / learning / response to cocaine / liver development / cellular response to nerve growth factor stimulus / visual learning / cytoplasmic side of plasma membrane / terminal bouton / response to estradiol / perikaryon / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of apoptotic process / receptor ligand activity / membrane raft / negative regulation of gene expression / axon / neuronal cell body / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / 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 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. ...Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / Neurotensin receptor / Neurotensin type 1 receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Neurotensin/neuromedin N / Neurotensin receptor type 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.57 Å
AuthorsEgloff, P. / Hillenbrand, M. / Scott, D.J. / Schlinkmann, K.M. / Heine, P. / Balada, S. / Batyuk, A. / Mittl, P. / Plueckthun, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of Signaling-Competent Neurotensin Receptor 1 Obtained by Directed Evolution in Escherichia Coli
Authors: Egloff, P. / Hillenbrand, M. / Klenk, C. / Batyuk, A. / Heine, P. / Balada, S. / Schlinkmann, K.M. / Scott, D.J. / Schuetz, M. / Plueckthun, A.
History
DepositionJul 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEUROTENSIN RECEPTOR TYPE 1
B: NEUROTENSIN RECEPTOR TYPE 1
C: NEUROTENSIN
D: NEUROTENSIN


Theoretical massNumber of molelcules
Total (without water)77,3714
Polymers77,3714
Non-polymers00
Water00
1
A: NEUROTENSIN RECEPTOR TYPE 1
C: NEUROTENSIN


Theoretical massNumber of molelcules
Total (without water)38,6852
Polymers38,6852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-5.7 kcal/mol
Surface area15320 Å2
MethodPISA
2
B: NEUROTENSIN RECEPTOR TYPE 1
D: NEUROTENSIN


Theoretical massNumber of molelcules
Total (without water)38,6852
Polymers38,6852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-6.5 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.880, 90.890, 211.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.4579, 0.1531, -0.875), (0.1512, -0.9573, -0.2464), (-0.8761, -0.2452, 0.4152)
Vector: 2.619, -31.16, -3.88)

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Components

#1: Protein NEUROTENSIN RECEPTOR TYPE 1 / NT-R-1 / NTR1 / HIGH-AFFINITY LEVOCABASTINE-INSENSITIVE NEUROTENSIN RECEPTOR / NTRH / NEUROTENSIN ...NT-R-1 / NTR1 / HIGH-AFFINITY LEVOCABASTINE-INSENSITIVE NEUROTENSIN RECEPTOR / NTRH / NEUROTENSIN RECEPTOR 1 HTGH4DIC3A


Mass: 37598.082 Da / Num. of mol.: 2 / Fragment: RESIDUES 50-390 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PEP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: P20789
#2: Protein/peptide NEUROTENSIN


Mass: 1087.277 Da / Num. of mol.: 2 / Fragment: C-TERMINUS, RESIDUES 157-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20068
Has protein modificationY
Sequence detailsCHAIN A, B HAS MUTATION AT FOLLOWING POSITIONS S83G,A86L, ...CHAIN A, B HAS MUTATION AT FOLLOWING POSITIONS S83G,A86L, S101R,H103D,H105Y,L119F,M121L,E124D,R143K,D150E,A161V, R167L,R213L,V234L,K235R,V240L,I253A,I260A,N262R, K263R,H305R,C332V,F342A,T354S,F358V,S362A.FURTHERMORE, CHAIN A, B IS A THERMOSTABLE MUTANT WITH INTRACELLULAR LOOP DELETION OF RESIDUES (T279-I295). FOR CHAINS C, D THE SEQUENCE RRPYIL CORRESPONDS TO RESIDUES 8-13 OF NEUROTENSIN. THE COMPLETE CRYSTALLIZED CONSTRUCT WAS GPGGRRPYIL (THE N-TERMINAL GPGG IS AN ARTIFICIAL LINKER. ONLY P10-I12 (CHAIN D) AND R8-I12 (CHAIN C) WERE 20 MODELLED.

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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: 3.88 Å3/Da / Density % sol: 68.34 % / Description: NONE
Crystal growpH: 5.5
Details: 20% (V/V) PEG600, 0.2 M CACL2, 50 MM NAACETATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.56→50 Å / Num. obs: 14522 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 174.88 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.88
Reflection shellResolution: 3.56→3.7 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 0.32 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BUO

4buo


Resolution: 3.57→21.88 Å / SU ML: 0.76 / σ(F): 1.35 / Phase error: 51.92 / Stereochemistry target values: ML / Details: PHENIX AND REFMAC WERE USED
RfactorNum. reflection% reflection
Rfree0.3449 648 5 %
Rwork0.3092 --
obs0.311 12954 89.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.57→21.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 0 0 4838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034957
X-RAY DIFFRACTIONf_angle_d0.7776758
X-RAY DIFFRACTIONf_dihedral_angle_d10.3821705
X-RAY DIFFRACTIONf_chiral_restr0.051819
X-RAY DIFFRACTIONf_plane_restr0.004813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5703-3.84460.5156770.52331435X-RAY DIFFRACTION53
3.8446-4.2290.44811320.39592516X-RAY DIFFRACTION93
4.229-4.83510.3861420.30942713X-RAY DIFFRACTION100
4.8351-6.07010.35091460.3492784X-RAY DIFFRACTION100
6.0701-21.87960.30671510.27362858X-RAY DIFFRACTION100

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