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- PDB-4buo: High Resolution Structure of Thermostable Agonist-bound Neurotens... -

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Basic information

Entry
Database: PDB / ID: 4buo
TitleHigh Resolution Structure of Thermostable 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


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 / positive regulation of gamma-aminobutyric acid secretion / D-aspartate import across plasma membrane ...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 / positive regulation of gamma-aminobutyric acid secretion / D-aspartate import across plasma membrane / 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 / positive regulation of glutamate secretion / G alpha (q) signalling events / hyperosmotic response / response to mineralocorticoid / response to food / positive regulation of inositol phosphate biosynthetic process / response to lipid / response to corticosterone / cellular response to lithium ion / temperature homeostasis / response to stress / detection of temperature stimulus involved in sensory perception of pain / associative learning / conditioned place preference / neuropeptide signaling pathway / cellular response to dexamethasone stimulus / response to axon injury / transport vesicle / axon terminus / positive regulation of release of sequestered calcium ion into cytosol / blood vessel diameter maintenance / response to amphetamine / adult locomotory behavior / dendritic shaft / 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 / membrane raft / receptor ligand activity / axon / negative regulation of gene expression / 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
GLYCINE / Neurotensin/neuromedin N / Neurotensin receptor type 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsEgloff, P. / Hillenbrand, M. / Schlinkmann, K.M. / 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
DepositionJun 21, 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,76415
Polymers76,9384
Non-polymers82611
Water00
1
A: NEUROTENSIN RECEPTOR TYPE 1
C: NEUROTENSIN/NEUROMEDIN N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,07010
Polymers38,4692
Non-polymers6018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-7.3 kcal/mol
Surface area14680 Å2
MethodPISA
2
B: NEUROTENSIN RECEPTOR TYPE 1
D: NEUROTENSIN/NEUROMEDIN N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6945
Polymers38,4692
Non-polymers2253
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-6.9 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.310, 89.400, 212.130
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
111(CHAIN A AND (RESSEQ 52:93 OR RESSEQ 97:270 OR RESSEQ 297:384))
211(CHAIN B AND (RESSEQ 49:91 OR RESSEQ 98:272 OR RESSEQ 291:386))
112CHAIN C
212CHAIN D

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.8974, -0.09648, 0.4305), (-0.05567, -0.9432, -0.3274), (0.4377, -0.3178, 0.8411)
Vector: 26.98, -22.54, -10.7)

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Components

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


Mass: 37381.926 Da / Num. of mol.: 2 / Fragment: RESIDUES 50-272 AND 291-390 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THERMOSTABLE MUTANT WITH INTRACELLULAR LOOP 3 DELETION B (E273-T290)
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 / NEUROTENSIN / NT


Mass: 1087.277 Da / Num. of mol.: 2 / Fragment: C-TERMINUS, RESIDUES 8-13
Source method: isolated from a genetically manipulated source
Details: RESIDUES 8-13 CORRESPOND TO NEUROTENSIN C- TERMINUS. RESIDUES 4-7 ARE PART OF AN ARTIFICIAL LINKER AND DO NOT CORRESPOND TO NEUROTENSIN SEQUENCE
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20068
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H5NO2
Has protein modificationY
Sequence detailsCHAINS C AND D - THE SEQUENCE RRPYIL REPRESENTS NEUROTENSIN RESIDUES 8-13 AND THE REST IS LINKER.

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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: 3.37 Å3/Da / Density % sol: 63.46 % / Description: NONE
Crystal growpH: 9.4 / Details: 21.5% (V/V) PEG600, 2 M NACL, 50 MM GLYCINE PH 9.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Aug 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 32141 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 109.97 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.85
Reflection shellResolution: 2.75→2.84 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 0.45 / % possible all: 88.7

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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: 2.75→19.821 Å / SU ML: 0.55 / σ(F): 1.35 / Phase error: 36.94 / Stereochemistry target values: ML / Details: PHENIX AND REFMAC WERE USED.
RfactorNum. reflection% reflection
Rfree0.2728 1581 5 %
Rwork0.2478 --
obs0.249 31649 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→19.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 55 0 5034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035160
X-RAY DIFFRACTIONf_angle_d0.6537020
X-RAY DIFFRACTIONf_dihedral_angle_d10.141774
X-RAY DIFFRACTIONf_chiral_restr0.047845
X-RAY DIFFRACTIONf_plane_restr0.003854
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 (%)
2.75-2.83860.47891220.46912374X-RAY DIFFRACTION88
2.8386-2.93970.45541430.43392677X-RAY DIFFRACTION99
2.9397-3.0570.40931440.39692740X-RAY DIFFRACTION100
3.057-3.19560.35211440.33542730X-RAY DIFFRACTION100
3.1956-3.36330.36821430.30712718X-RAY DIFFRACTION100
3.3633-3.57290.32571450.27582754X-RAY DIFFRACTION100
3.5729-3.84690.28991440.25612748X-RAY DIFFRACTION100
3.8469-4.23060.25911470.22862788X-RAY DIFFRACTION100
4.2306-4.8350.22281460.20482784X-RAY DIFFRACTION100
4.835-6.06250.26571480.24012805X-RAY DIFFRACTION100
6.0625-19.82160.25271550.23212950X-RAY DIFFRACTION100

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