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- PDB-6hll: Crystal structure of the Neurokinin 1 receptor in complex with th... -

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Basic information

Entry
Database: PDB / ID: 6hll
TitleCrystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist CP-99,994
ComponentsSubstance-P receptor,GlgA glycogen synthase,Substance-P receptor
KeywordsMEMBRANE PROTEIN / 7-TM / GPCR / Signalling protein
Function / homology
Function and homology information


substance P receptor activity / tachykinin receptor activity / positive regulation of flagellated sperm motility / aggressive behavior / Tachykinin receptors bind tachykinins / sperm ejaculation / positive regulation of uterine smooth muscle contraction / positive regulation of synaptic transmission, cholinergic / detection of abiotic stimulus / operant conditioning ...substance P receptor activity / tachykinin receptor activity / positive regulation of flagellated sperm motility / aggressive behavior / Tachykinin receptors bind tachykinins / sperm ejaculation / positive regulation of uterine smooth muscle contraction / positive regulation of synaptic transmission, cholinergic / detection of abiotic stimulus / operant conditioning / positive regulation of lymphocyte proliferation / tachykinin receptor signaling pathway / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / response to ozone / sperm head / positive regulation of action potential / response to auditory stimulus / positive regulation of blood pressure / smooth muscle contraction involved in micturition / regulation of smooth muscle cell proliferation / positive regulation of vascular permeability / positive regulation of hormone secretion / positive regulation of ossification / regulation of smooth muscle cell migration / positive regulation of leukocyte migration / eating behavior / positive regulation of vasoconstriction / behavioral response to pain / angiotensin-mediated drinking behavior / associative learning / positive regulation of epithelial cell migration / response to electrical stimulus / long-term memory / sperm flagellum / positive regulation of stress fiber assembly / sperm midpiece / response to progesterone / positive regulation of epithelial cell proliferation / positive regulation of synaptic transmission, GABAergic / response to nicotine / response to estradiol / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of cytosolic calcium ion concentration / cell body / response to ethanol / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / postsynaptic membrane / inflammatory response / dendrite / cell surface / plasma membrane
Similarity search - Function
Neurokinin NK1 receptor / Neurokinin receptor / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Neurokinin NK1 receptor / Neurokinin receptor / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / 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) / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GBK / Substance-P receptor / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsSchoppe, J. / Ehrenmann, J. / Klenk, C. / Rucktooa, P. / Schutz, M. / Dore, A.S. / Pluckthun, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_153143 Switzerland
CitationJournal: Nat Commun / Year: 2019
Title: Crystal structures of the human neurokinin 1 receptor in complex with clinically used antagonists.
Authors: Schoppe, J. / Ehrenmann, J. / Klenk, C. / Rucktooa, P. / Schutz, M. / Dore, A.S. / Pluckthun, A.
History
DepositionSep 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.2Jan 24, 2024Group: 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Substance-P receptor,GlgA glycogen synthase,Substance-P receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3302
Polymers59,0341
Non-polymers2961
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein elutes as a monomer from size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.996, 122.733, 286.494
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Substance-P receptor,GlgA glycogen synthase,Substance-P receptor / SPR / NK-1 receptor / NK-1R / Tachykinin receptor 1 / Glycogen synthase / SPR / NK-1 receptor / NK- ...SPR / NK-1 receptor / NK-1R / Tachykinin receptor 1 / Glycogen synthase / SPR / NK-1 receptor / NK-1R / Tachykinin receptor 1


Mass: 59034.059 Da / Num. of mol.: 1
Mutation: L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi GE5 (archaea)
Gene: TACR1, NK1R, TAC1R, PAB2292 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25103, UniProt: Q9V2J8
#2: Chemical ChemComp-GBK / (2~{S},3~{S})-~{N}-[(2-methoxyphenyl)methyl]-2-phenyl-piperidin-3-amine


Mass: 296.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N2O
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: 5.12 Å3/Da / Density % sol: 76 % / Description: Needle-like
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 100 mM MES pH 6.0, 31% (v/v) PEG400, 190-210 mM potassium acetate, 2.4% (v/v) 2,5-hexanediol and 50 uM CP-99,994

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2017 / Details: Mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 3.27→47.88 Å / Num. obs: 17430 / % possible obs: 99.9 % / Redundancy: 32.2 % / CC1/2: 0.99 / Rpim(I) all: 0.125 / Net I/σ(I): 5.1
Reflection shellResolution: 3.27→3.53 Å / Redundancy: 29.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3479 / CC1/2: 0.311 / Rpim(I) all: 0.886 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZJC

4zjc


Resolution: 3.27→24.916 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 874 5.04 %
Rwork0.2253 --
obs0.2278 17325 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.27→24.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3754 0 22 0 3776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043877
X-RAY DIFFRACTIONf_angle_d0.9115254
X-RAY DIFFRACTIONf_dihedral_angle_d12.4212266
X-RAY DIFFRACTIONf_chiral_restr0.057597
X-RAY DIFFRACTIONf_plane_restr0.006640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2702-3.47460.37541420.33392675X-RAY DIFFRACTION100
3.4746-3.7420.31511420.28752694X-RAY DIFFRACTION100
3.742-4.11710.28521420.25082730X-RAY DIFFRACTION100
4.1171-4.70940.26541430.21082722X-RAY DIFFRACTION100
4.7094-5.92010.24381580.19582744X-RAY DIFFRACTION100
5.9201-24.91650.25561470.19092886X-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)
10.72240.52160.63420.46620.72430.89410.0580.11780.0655-0.0949-0.02150.0777-0.00360.04990.00140.5760.1002-0.10630.6306-0.07250.33615.067517.5616-41.2069
20.432-0.3758-0.34020.8037-0.07130.98950.103-0.1831-0.0743-0.0244-0.00130.1479-0.16530.064200.28790.0606-0.00760.2489-0.03040.4677-1.862241.03033.7033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 1232 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1233 through 1413 )

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