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

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Basic information

Entry
Database: PDB / ID: 6hlo
TitleCrystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist Aprepitant
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 / positive regulation of uterine smooth muscle contraction / positive regulation of synaptic transmission, cholinergic / detection of abiotic stimulus / tachykinin receptor signaling pathway / operant conditioning ...substance P receptor activity / tachykinin receptor activity / positive regulation of flagellated sperm motility / aggressive behavior / Tachykinin receptors bind tachykinins / positive regulation of uterine smooth muscle contraction / positive regulation of synaptic transmission, cholinergic / detection of abiotic stimulus / tachykinin receptor signaling pathway / operant conditioning / positive regulation of lymphocyte proliferation / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / sperm head / response to ozone / sperm ejaculation / positive regulation of action potential / response to auditory stimulus / regulation of smooth muscle cell proliferation / smooth muscle contraction involved in micturition / positive regulation of blood pressure / positive regulation of hormone secretion / positive regulation of vascular permeability / regulation of smooth muscle cell migration / positive regulation of ossification / positive regulation of leukocyte migration / eating behavior / positive regulation of epithelial cell migration / behavioral response to pain / associative learning / angiotensin-mediated drinking behavior / sperm flagellum / response to electrical stimulus / long-term memory / positive regulation of vasoconstriction / positive regulation of stress fiber assembly / sperm midpiece / positive regulation of epithelial cell proliferation / response to progesterone / positive regulation of synaptic transmission, GABAergic / response to nicotine / Cargo recognition for clathrin-mediated endocytosis / response to estradiol / Clathrin-mediated endocytosis / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / cell body / G alpha (q) signalling events / response to ethanol / 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 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM ...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 / 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)
Similarity search - Domain/homology
CITRIC ACID / Chem-GBQ / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Substance-P receptor / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)65,74623
Polymers59,1481
Non-polymers6,59822
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein elutes as a monomeric peak on size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint30 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.189, 76.450, 167.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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: 59148.160 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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25103, UniProt: Q9V2J8

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Non-polymers , 5 types, 96 molecules

#2: Chemical ChemComp-GBQ / 5-[[(2~{R},3~{S})-2-[(1~{R})-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy]-3-(4-fluorophenyl)morpholin-4-yl]methyl]-1,2-dihydro-1,2,4-triazol-3-one


Mass: 534.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21F7N4O3 / Comment: medication, chemotherapy*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 66.56 % / Description: Star-shaped
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 100 mM sodium citrate pH 6.0, 31% (v/v) PEG400, 50-70 mM MgCl2 and 50 uM aprepitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2017 / Details: Mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.24 Å / Num. obs: 32007 / % possible obs: 100 % / Redundancy: 26.2 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 12.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 26.4 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3297 / CC1/2: 0.753 / Rpim(I) all: 0.571 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZJC

4zjc


Resolution: 2.4→29.442 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2293 1656 5.19 %
Rwork0.2006 --
obs0.2021 31899 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 315 74 4221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034228
X-RAY DIFFRACTIONf_angle_d0.5785652
X-RAY DIFFRACTIONf_dihedral_angle_d13.4052510
X-RAY DIFFRACTIONf_chiral_restr0.044614
X-RAY DIFFRACTIONf_plane_restr0.005684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47060.35951320.28322463X-RAY DIFFRACTION100
2.4706-2.55030.30841360.25382495X-RAY DIFFRACTION100
2.5503-2.64140.30461320.23472470X-RAY DIFFRACTION100
2.6414-2.74710.29131270.22322495X-RAY DIFFRACTION100
2.7471-2.8720.29231220.22132499X-RAY DIFFRACTION100
2.872-3.02330.29951260.222497X-RAY DIFFRACTION100
3.0233-3.21250.24541390.21072505X-RAY DIFFRACTION100
3.2125-3.46020.25591460.20582519X-RAY DIFFRACTION100
3.4602-3.80770.20611450.1932508X-RAY DIFFRACTION100
3.8077-4.35720.22131410.18162534X-RAY DIFFRACTION100
4.3572-5.48380.18531690.18092554X-RAY DIFFRACTION100
5.4838-29.44390.20861410.19662704X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.0027 Å / Origin y: -11.0178 Å / Origin z: 58.478 Å
111213212223313233
T0.4715 Å20.0162 Å20.0015 Å2-0.4783 Å2-0.0521 Å2--0.5428 Å2
L0.4562 °2-0.1691 °20.3962 °2-1.2796 °2-1.7452 °2--3.2033 °2
S0.0552 Å °-0.0371 Å °0.0089 Å °0.006 Å °0.0138 Å °0.0592 Å °0.0326 Å °0.1057 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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