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- PDB-3zev: Structure of Thermostable Agonist-bound Neurotensin Receptor 1 Mu... -

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Basic information

Entry
Database: PDB / ID: 3zev
TitleStructure of Thermostable Agonist-bound Neurotensin Receptor 1 Mutant without Lysozyme Fusion
Components
  • NEUROTENSIN
  • NEUROTENSIN RECEPTOR 1 TM86V
KeywordsSIGNALING PROTEIN / 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 / positive regulation of arachidonate secretion / neuron spine / L-glutamate import across plasma membrane / regulation of respiratory gaseous exchange / positive regulation of inhibitory postsynaptic potential / neuropeptide hormone activity / hyperosmotic response / negative regulation of systemic arterial blood pressure / positive regulation of glutamate secretion / negative regulation of release of sequestered calcium ion into cytosol / digestive tract development / G alpha (q) signalling events / response to corticosterone / positive regulation of inositol phosphate biosynthetic process / response to lipid / cellular response to lithium ion / temperature homeostasis / detection of temperature stimulus involved in sensory perception of pain / response to axon injury / neuropeptide signaling pathway / transport vesicle / axon terminus / response to amphetamine / cellular response to dexamethasone stimulus / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / blood vessel diameter maintenance / liver development / adult locomotory behavior / learning / response to cocaine / cellular response to nerve growth factor stimulus / terminal bouton / visual learning / cytoplasmic side of plasma membrane / response to estradiol / dendritic spine / perikaryon / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of apoptotic process / receptor ligand activity / membrane raft / axon / negative regulation of gene expression / neuronal cell body / dendrite / positive regulation of gene expression / protein-containing complex binding / 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
GLYCINE / Neurotensin/neuromedin N / Neurotensin receptor type 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 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
DepositionDec 7, 2012Deposition 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 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUROTENSIN RECEPTOR 1 TM86V
B: NEUROTENSIN RECEPTOR 1 TM86V
C: NEUROTENSIN
D: NEUROTENSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4569
Polymers77,0804
Non-polymers3755
Water00
1
B: NEUROTENSIN RECEPTOR 1 TM86V
D: NEUROTENSIN


Theoretical massNumber of molelcules
Total (without water)38,5402
Polymers38,5402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-8.1 kcal/mol
Surface area15060 Å2
MethodPISA
2
A: NEUROTENSIN RECEPTOR 1 TM86V
C: NEUROTENSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9167
Polymers38,5402
Non-polymers3755
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-6.9 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.550, 90.180, 209.360
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: (-0.51, 0.1456, 0.8478), (0.1472, -0.9563, 0.2528), (0.8475, 0.2537, 0.4663)
Vector: -3.92, 28.8, -2.834)

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Components

#1: Protein NEUROTENSIN RECEPTOR 1 TM86V


Mass: 37607.113 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THERMOSTABLE MUTANT / 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


Mass: 933.111 Da / Num. of mol.: 2 / Fragment: C-TERMINUS, RESIDUES 157-162
Source method: isolated from a genetically manipulated source
Details: RESIDUES 8-13 CORRESPOND TO NEUROTENSIN C-TERMINUS. RESIDUES 6-7 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.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
Has protein modificationY

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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: 3.68 Å3/Da / Density % sol: 66.54 % / Description: NONE
Crystal growpH: 9.4
Details: 1.28% (W/V) NONYL-GLUCOSIDE, 0.5% (W/V) DECYL-GLUCOSIDE, 0.01% (W/V) DODECYL-GLUCOSIDE, 0.1% (W/V) CHOLESTERYLHEMISUCCINATE, 10MM HEPES PH 8, 1.15 MM NACL, 2 MM DTT, 100 NM NTI, 26% (V/V) ...Details: 1.28% (W/V) NONYL-GLUCOSIDE, 0.5% (W/V) DECYL-GLUCOSIDE, 0.01% (W/V) DODECYL-GLUCOSIDE, 0.1% (W/V) CHOLESTERYLHEMISUCCINATE, 10MM HEPES PH 8, 1.15 MM NACL, 2 MM DTT, 100 NM NTI, 26% (V/V) PEG 600, 50 MM GLYCINE PH 9.4

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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→50 Å / Num. obs: 22942 / % possible obs: 99.8 % / Observed criterion σ(I): 0.72 / Redundancy: 6.9 % / Biso Wilson estimate: 115.97 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 8.68

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3→19.935 Å / SU ML: 0.39 / σ(F): 1.33 / Phase error: 32.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2792 1129 5 %
Rwork0.2418 --
obs0.2436 22639 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 125.7 Å2
Refinement stepCycle: LAST / Resolution: 3→19.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4931 0 25 0 4956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035073
X-RAY DIFFRACTIONf_angle_d0.7356912
X-RAY DIFFRACTIONf_dihedral_angle_d10.7911748
X-RAY DIFFRACTIONf_chiral_restr0.047838
X-RAY DIFFRACTIONf_plane_restr0.003834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0003-3.13640.39551430.36762425X-RAY DIFFRACTION92
3.1364-3.3010.37641230.33422687X-RAY DIFFRACTION100
3.301-3.50680.3481440.28642682X-RAY DIFFRACTION100
3.5068-3.77590.29091350.25042666X-RAY DIFFRACTION100
3.7759-4.15270.25811470.22662708X-RAY DIFFRACTION100
4.1527-4.74660.27581400.20462725X-RAY DIFFRACTION100
4.7466-5.95360.27661450.25112750X-RAY DIFFRACTION100
5.9536-19.93550.25811520.23342867X-RAY DIFFRACTION100
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)
12.44360.33180.09013.57220.25094.0092-0.0903-0.12110.40250.1720.123-0.4874-0.21290.7034-0.04140.7062-0.1382-0.0670.7279-0.14490.7648-11.152224.303-31.2116
23.96970.65820.79864.90290.78794.9490.0122-0.6609-0.28161.03010.10630.03470.66450.0142-0.17130.72730.0421-0.09850.74160.13560.5979-20.9055-4.016-20.5944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 51:386)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 51:386)

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