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- PDB-6j20: Crystal structure of the human NK1 substance P receptor -

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Basic information

Entry
Database: PDB / ID: 6j20
TitleCrystal structure of the human NK1 substance P receptor
ComponentsSubstance-P receptor,Endolysin
KeywordsMEMBRANE PROTEIN / GPCR / Complex / Antagonist / 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 / detection of abiotic stimulus / positive regulation of synaptic transmission, cholinergic / operant conditioning / sperm head ...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 / detection of abiotic stimulus / positive regulation of synaptic transmission, cholinergic / operant conditioning / sperm head / sperm ejaculation / positive regulation of lymphocyte proliferation / tachykinin receptor signaling pathway / response to ozone / response to auditory stimulus / positive regulation of action potential / smooth muscle contraction involved in micturition / positive regulation of blood pressure / regulation of smooth muscle cell proliferation / positive regulation of hormone secretion / positive regulation of vascular permeability / positive regulation of ossification / regulation of smooth muscle cell migration / positive regulation of leukocyte migration / eating behavior / positive regulation of epithelial cell migration / behavioral response to pain / angiotensin-mediated drinking behavior / associative learning / long-term memory / sperm flagellum / response to electrical stimulus / positive regulation of vasoconstriction / viral release from host cell by cytolysis / positive regulation of stress fiber assembly / sperm midpiece / peptidoglycan catabolic process / response to progesterone / response to nicotine / positive regulation of epithelial cell proliferation / positive regulation of synaptic transmission, GABAergic / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / response to estradiol / lysozyme / Clathrin-mediated endocytosis / cell body / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / response to ethanol / host cell cytoplasm / defense response to bacterium / inflammatory response / dendrite / cell surface / plasma membrane
Similarity search - Function
Neurokinin NK1 receptor / Neurokinin 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 ...Neurokinin NK1 receptor / Neurokinin 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
Chem-GBQ / Endolysin / Substance-P receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen, S. / Lu, M. / Zhang, H. / Wu, B. / Zhao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDB-SSW-SMC054 China
CitationJournal: Nat Commun / Year: 2019
Title: Human substance P receptor binding mode of the antagonist drug aprepitant by NMR and crystallography.
Authors: Chen, S. / Lu, M. / Liu, D. / Yang, L. / Yi, C. / Ma, L. / Zhang, H. / Liu, Q. / Frimurer, T.M. / Wang, M.W. / Schwartz, T.W. / Stevens, R.C. / Wu, B. / Wuthrich, K. / Zhao, Q.
History
DepositionDec 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Substance-P receptor,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0192
Polymers50,4851
Non-polymers5341
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20800 Å2
Unit cell
Length a, b, c (Å)102.512, 102.512, 156.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Substance-P receptor,Endolysin / SPR / NK-1 receptor / NK-1R / Tachykinin receptor 1 / Lysis protein / Lysozyme / Muramidase


Mass: 50484.844 Da / Num. of mol.: 1 / Mutation: E78N,Y121W,T222R,C97A
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Substance-P receptor NK1R (residues 2-226), mini-T4L (residues 1001-1010, 1017-1117), LINKER GGGSGG (residues 1011-1016), and NK1R (residues 237-335)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: TACR1, NK1R, TAC1R, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25103, UniProt: D9IEF7, lysozyme
#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 / Aprepitant


Mass: 534.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21F7N4O3 / Comment: medication, chemotherapy*YM

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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: 4.08 Å3/Da / Density % sol: 69.88 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100mM MES, pH 6.0-6.6, 25-35% PEG 400, 200-350mM ammonium tartrate dibasic
PH range: 6.0-6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26005 / % possible obs: 99 % / Redundancy: 9.2 % / Biso Wilson estimate: 101.91 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 0.99 / Num. unique obs: 2240 / CC1/2: 0.5 / % possible all: 60

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GRV, 4U15

4grv

4u15


Resolution: 2.7→46.6 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.922 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.339 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.334 / SU Rfree Blow DPI: 0.253 / SU Rfree Cruickshank DPI: 0.257
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1201 5.08 %RANDOM
Rwork0.233 ---
obs0.234 23622 99.8 %-
Displacement parametersBiso mean: 114.89 Å2
Baniso -1Baniso -2Baniso -3
1--9.1286 Å20 Å20 Å2
2---9.1286 Å20 Å2
3---18.2572 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: 1 / Resolution: 2.7→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 37 0 3184
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093277HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14490HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1041SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes481HARMONIC5
X-RAY DIFFRACTIONt_it3277HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion19.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion442SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3746SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.247 126 4.54 %
Rwork0.209 2648 -
all0.21 2774 -
obs--98.68 %
Refinement TLS params.Method: refined / Origin x: -86.8273 Å / Origin y: 55.3825 Å / Origin z: 343.906 Å
111213212223313233
T-0.4676 Å20.0604 Å2-0.0147 Å2--0.222 Å20.1099 Å2---0.4724 Å2
L0.0307 °20.4222 °20.5839 °2-1.4075 °21.7571 °2--4.8976 °2
S0.036 Å °0.0534 Å °0.0278 Å °-0.0904 Å °-0.1728 Å °-0.1261 Å °-0.5015 Å °0.7599 Å °0.1368 Å °
Refinement TLS groupSelection details: { A|* }

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