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- PDB-5t04: STRUCTURE OF CONSTITUTIVELY ACTIVE NEUROTENSIN RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 5t04
TitleSTRUCTURE OF CONSTITUTIVELY ACTIVE NEUROTENSIN RECEPTOR
Components
  • ARG-ARG-PRO-TYR-ILE-LEU
  • Neurotensin receptor type 1,Endolysin,Neurotensin receptor type 1
KeywordsSIGNALING PROTEIN / MEMBRANE PROTEIN / G PROTEIN-COUPLED RECEPTOR / GPCR / NEUROTENSIN RECEPTOR / NTSR1 / agonist
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 / viral release from host cell by cytolysis / transport vesicle / response to amphetamine / blood vessel diameter maintenance / peptidoglycan catabolic process / 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 / cell wall macromolecule catabolic process / lysozyme / response to estradiol / lysozyme activity / perikaryon / host cell cytoplasm / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / defense response to bacterium / 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 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / G-protein coupled receptors family 1 signature. ...Neurotensin/neuromedin N / Neurotensin/neuromedin N precursor / Neurotensin receptor / Neurotensin type 1 receptor / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 3,3',3''-phosphanetriyltripropanoic acid / 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: 3.3 Å
AuthorsKrumm, B. / Botos, I. / Grisshammer, R.
CitationJournal: Sci Rep / Year: 2016
Title: Structure and dynamics of a constitutively active neurotensin receptor.
Authors: Krumm, B.E. / Lee, S. / Bhattacharya, S. / Botos, I. / White, C.F. / Du, H. / Vaidehi, N. / Grisshammer, R.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotensin receptor type 1,Endolysin,Neurotensin receptor type 1
B: ARG-ARG-PRO-TYR-ILE-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0937
Polymers58,4322
Non-polymers6615
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-5 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.190, 75.710, 83.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Neurotensin receptor type 1,Endolysin,Neurotensin receptor type 1 / NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH / Lysis protein / ...NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH / Lysis protein / Lysozyme / Muramidase / NTR1 / High-affinity levocabastine-insensitive neurotensin receptor / NTRH


Mass: 57613.445 Da / Num. of mol.: 1
Fragment: unp residues 43-268; 2-161; 297-396,unp residues 43-268; 2-161; 297-396,unp residues 43-268; 2-161; 297-396
Mutation: A86L, G215A, F358A, V360A, R12G, C54T, C97A, Q122N, Q123N, I137R,A86L, G215A, F358A, V360A, R12G, C54T, C97A, Q122N, Q123N, I137R,A86L, G215A, F358A, V360A, R12G, C54T, C97A, Q122N, Q123N, I137R
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 ARG-ARG-PRO-TYR-ILE-LEU


Mass: 819.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P20068*PLUS
#3: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3

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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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 13-16% (v/v) PEG 400, 80 mM TrisHCl pH 8.5-9.0, 1.9 mM TCEP, 68-91 mM lithium acetate, 0.9 mM Neurotensin
PH range: 8.5-9.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.0332
SYNCHROTRONAPS 23-ID-B21.0332
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJun 25, 2015
MARMOSAIC 300 mm CCD2CCDFeb 26, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
21
ReflectionResolution: 3.3→38.141 Å / Num. obs: 10042 / % possible obs: 97.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.3
Reflection shellResolution: 3.3→3.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.6 / % possible all: 88.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XEE

4xee


Resolution: 3.3→38.141 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 30.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2833 1484 7.99 %
Rwork0.253 --
obs0.2555 18582 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→38.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 43 0 3703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023781
X-RAY DIFFRACTIONf_angle_d0.4945130
X-RAY DIFFRACTIONf_dihedral_angle_d12.5612228
X-RAY DIFFRACTIONf_chiral_restr0.039597
X-RAY DIFFRACTIONf_plane_restr0.005634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3003-3.40680.36241240.35231354X-RAY DIFFRACTION86
3.4068-3.52850.36281280.32241375X-RAY DIFFRACTION88
3.5285-3.66960.29431260.30671610X-RAY DIFFRACTION99
3.6696-3.83650.34271360.29731596X-RAY DIFFRACTION100
3.8365-4.03860.33941530.28141594X-RAY DIFFRACTION100
4.0386-4.29130.29781240.25681607X-RAY DIFFRACTION100
4.2913-4.62210.31591470.24971571X-RAY DIFFRACTION100
4.6221-5.08630.2911570.24611574X-RAY DIFFRACTION100
5.0863-5.820.3767990.26821635X-RAY DIFFRACTION100
5.82-7.32410.2851410.25311594X-RAY DIFFRACTION100
7.3241-38.14390.17541490.18831588X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 228.6574 Å / Origin y: 16.6097 Å / Origin z: 96.5727 Å
111213212223313233
T0.6506 Å2-0.0298 Å20.0376 Å2-0.3866 Å20.0691 Å2--0.609 Å2
L1.7744 °21.0331 °22.1998 °2-0.6489 °21.3564 °2--3.5909 °2
S-0.0182 Å °-0.0725 Å °0.0265 Å °0.1158 Å °-0.0393 Å °0.0096 Å °-0.1396 Å °-0.1072 Å °0.0805 Å °
Refinement TLS groupSelection details: all

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