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- PDB-4bv0: High Resolution Structure of Evolved Agonist-bound Neurotensin Re... -

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Basic information

Entry
Database: PDB / ID: 4bv0
TitleHigh Resolution Structure of Evolved Agonist-bound Neurotensin Receptor 1 Mutant without Lysozyme Fusion
Components
  • NEUROTENSIN RECEPTOR TYPE 1
  • NEUROTENSIN/NEUROMEDIN N
KeywordsSIGNALING PROTEIN / G PROTEIN COUPLED RECEPTOR / MEMBRANE PROTEIN
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 / symmetric synapse / response to mineralocorticoid / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / regulation of membrane depolarization ...response to antipsychotic drug / Peptide ligand-binding receptors / neuropeptide receptor binding / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / response to mineralocorticoid / 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 / neuron spine / positive regulation of inhibitory postsynaptic potential / neuropeptide hormone activity / hyperosmotic response / digestive tract development / negative regulation of systemic arterial blood pressure / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of glutamate secretion / G alpha (q) signalling events / positive regulation of inositol phosphate biosynthetic process / temperature homeostasis / response to corticosterone / response to lipid / cellular response to lithium ion / detection of temperature stimulus involved in sensory perception of pain / response to axon injury / neuropeptide signaling pathway / axon terminus / transport vesicle / response to amphetamine / blood vessel diameter maintenance / adult locomotory behavior / cellular response to dexamethasone stimulus / positive regulation of release of sequestered calcium ion into cytosol / cellular response to nerve growth factor stimulus / liver development / response to cocaine / dendritic shaft / learning / visual learning / terminal bouton / cytoplasmic side of plasma membrane / response to estradiol / perikaryon / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / positive regulation of apoptotic process / membrane raft / axon / negative regulation of gene expression / neuronal cell body / dendrite / 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 / 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: 3.1 Å
AuthorsEgloff, P. / Hillenbrand, M. / Scott, D.J. / Schlinkmann, K.M. / Heine, P. / Balada, S. / Batyuk, A. / Mittl, P. / Schuetz, M. / 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
DepositionJun 24, 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 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.page_last / _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Dec 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

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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/NEUROMEDIN N
D: NEUROTENSIN/NEUROMEDIN N


Theoretical massNumber of molelcules
Total (without water)77,6134
Polymers77,6134
Non-polymers00
Water00
1
A: NEUROTENSIN RECEPTOR TYPE 1
C: NEUROTENSIN/NEUROMEDIN N


Theoretical massNumber of molelcules
Total (without water)38,8072
Polymers38,8072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-8.1 kcal/mol
Surface area14650 Å2
MethodPISA
2
B: NEUROTENSIN RECEPTOR TYPE 1
D: NEUROTENSIN/NEUROMEDIN N


Theoretical massNumber of molelcules
Total (without water)38,8072
Polymers38,8072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-7.1 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.580, 91.560, 208.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B
112CHAIN C
212CHAIN D

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.488, -0.155, -0.859), (-0.1464, -0.9556, 0.2556), (-0.8604, 0.2505, 0.4437)
Vector: -4.465, -30.54, 2.75)

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Components

#1: Protein NEUROTENSIN RECEPTOR TYPE 1 / NEUROTENSIN RECEPTOR 1 TM86VDIC3B / NT-R-1 / NTR1 / HIGH-AFFINITY LEVOCABASTINE-INSENSITIVE ...NEUROTENSIN RECEPTOR 1 TM86VDIC3B / NT-R-1 / NTR1 / HIGH-AFFINITY LEVOCABASTINE-INSENSITIVE NEUROTENSIN RECEPTOR / NTRH


Mass: 37719.238 Da / Num. of mol.: 2 / Fragment: RESIDUES 50-390 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THERMOSTABLE MUTANT WITH INTRACELLULAR LOOP 3 DELETION B (T279-I295)
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PEP-TM86VDIC3III / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: P20789
#2: Protein/peptide NEUROTENSIN/NEUROMEDIN N / LARGE NEUROMEDIN N / NMN-125 / NEUROMEDIN N / NN / NMN / NEUROTENSIN / NT / TAIL PEPTIDE


Mass: 1087.277 Da / Num. of mol.: 2 / Fragment: C-TERMINUS, RESIDUES 157-162
Source method: isolated from a genetically manipulated source
Details: THE SEQUENCE RRPYIL CORRESPONDS TO RESIDUES 8-13 OF THE NEUROTENSIN C-TERMINUS. THE FULL CRYSTALLIZED CONSTRUCT WAS GPGGRRPYIL (THE N-TERMINAL GPGG IS AN ARTIFICIAL LINKER).
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20068

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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: 3.73 Å3/Da / Density % sol: 67.03 % / Description: NONE
Crystal growpH: 9.4
Details: 22.5% (V/V) PEG600, 0.5 M NACL, 50 MM GLYCINE PH 9.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Type: SLS / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 21665 / % possible obs: 99.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.55
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 0.51 / % possible all: 97

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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 3ZEV

3zev


Resolution: 3.1→19.88 Å / SU ML: 0.77 / σ(F): 1.35 / Phase error: 45.01 / Stereochemistry target values: ML / Details: PHENIX AND REFMAC WERE USED
RfactorNum. reflection% reflection
Rfree0.3105 1036 5 %
Rwork0.284 --
obs-20680 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4865 0 0 0 4865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034985
X-RAY DIFFRACTIONf_angle_d0.6516794
X-RAY DIFFRACTIONf_dihedral_angle_d10.1051725
X-RAY DIFFRACTIONf_chiral_restr0.046821
X-RAY DIFFRACTIONf_plane_restr0.003818
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
21CX-RAY DIFFRACTIONPOSITIONAL
22DX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1002-3.2630.44841370.44852589X-RAY DIFFRACTION89
3.263-3.46650.44711400.45342635X-RAY DIFFRACTION92
3.4665-3.73250.47621330.42682512X-RAY DIFFRACTION86
3.7325-4.10510.34581510.33792899X-RAY DIFFRACTION99
4.1051-4.69230.29041550.23952934X-RAY DIFFRACTION100
4.6923-5.88620.28641560.26282967X-RAY DIFFRACTION100
5.8862-19.87650.26551640.23753108X-RAY DIFFRACTION100

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