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- PDB-6e59: Crystal structure of the human NK1 tachykinin receptor -

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Basic information

Entry
Database: PDB / ID: 6.0E+59
TitleCrystal structure of the human NK1 tachykinin receptor
ComponentsSubstance-P receptor, GlgA glycogen synthase, Substance-P receptor chimera
KeywordsSIGNALING PROTEIN / G Protein-Coupled Receptor Fusion Protein
Function / homology
Function and homology information


substance P receptor activity / tachykinin receptor activity / aggressive behavior / Tachykinin receptors bind tachykinins / positive regulation of flagellated sperm motility / positive regulation of uterine smooth muscle contraction / detection of abiotic stimulus / positive regulation of synaptic transmission, cholinergic / tachykinin receptor signaling pathway / positive regulation of lymphocyte proliferation ...substance P receptor activity / tachykinin receptor activity / aggressive behavior / Tachykinin receptors bind tachykinins / positive regulation of flagellated sperm motility / positive regulation of uterine smooth muscle contraction / detection of abiotic stimulus / positive regulation of synaptic transmission, cholinergic / tachykinin receptor signaling pathway / positive regulation of lymphocyte proliferation / operant conditioning / sperm head / glycogen (starch) synthase activity / response to ozone / sperm ejaculation / positive regulation of action potential / response to auditory stimulus / smooth muscle contraction involved in micturition / regulation of smooth muscle cell proliferation / positive regulation of hormone secretion / positive regulation of blood pressure / positive regulation of vascular permeability / positive regulation of ossification / regulation of smooth muscle cell migration / glycogen biosynthetic process / 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 / long-term memory / response to electrical stimulus / positive regulation of vasoconstriction / sperm midpiece / positive regulation of stress fiber assembly / 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 / cell body / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / response to ethanol / inflammatory response / dendrite / cell surface / plasma membrane / cytosol
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
Chem-L76 / Substance-P receptor / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsYin, J. / Clark, L. / Chapman, K. / Shao, Z. / Borek, D. / Xu, Q. / Wang, J. / Rosenbaum, D.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01-NS103939 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM079383 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21-GM097617 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Crystal structure of the human NK1tachykinin receptor.
Authors: Yin, J. / Chapman, K. / Clark, L.D. / Shao, Z. / Borek, D. / Xu, Q. / Wang, J. / Rosenbaum, D.M.
History
DepositionJul 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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, GlgA glycogen synthase, Substance-P receptor chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4502
Polymers61,8741
Non-polymers5761
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.789, 61.975, 142.942
Angle α, β, γ (deg.)90.000, 100.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 61874.176 Da / Num. of mol.: 1
Fragment: receptor (UNP residues 1-227, 238-346) with intervening glycogen synthase (UNP residues 218-413)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Gene: TACR1, NK1R, TAC1R, PAB2292 / Strain: GE5 / Orsay
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: P25103, UniProt: Q9V2J8
#2: Chemical ChemComp-L76 / 1-(4-{[(2R,3S)-2-{(1R)-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy}-3-(4-fluorophenyl)morpholin-4-yl]methyl}-1H-1,2,3-triazol-5-yl)-N,N-dimethylmethanamine


Mass: 575.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28F7N5O2

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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: 4.37 Å3/Da / Density % sol: 71.83 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM sodium citrate, pH 5.4, 30% PEG300, 200 mM potassium nitrate, 2% 2,5-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 18, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.4→34.44 Å / Num. obs: 11937 / % possible obs: 94.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 6.97
Reflection shellResolution: 3.4→3.46 Å / CC1/2: 0.41 / Rpim(I) all: 0.577

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZJ8

4zj8


Resolution: 3.4→34.44 Å / Cor.coef. Fo:Fc: 0.846 / Cor.coef. Fo:Fc free: 0.756 / SU B: 67.704 / SU ML: 0.498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.667 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3048 586 4.9 %RANDOM
Rwork0.2483 ---
obs0.2511 11310 79.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 358.24 Å2 / Biso mean: 65.516 Å2 / Biso min: 5.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20.06 Å2
2---0.4 Å20 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 3.4→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 1572 0 5416
Biso mean--21.39 --
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133992
X-RAY DIFFRACTIONr_bond_other_d0.0070.0173802
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.6455425
X-RAY DIFFRACTIONr_angle_other_deg1.5341.5778757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66721.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73415670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0231520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024342
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02910
LS refinement shellResolution: 3.4→3.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 15 -
Rwork0.268 263 -
all-278 -
obs--25.02 %
Refinement TLS params.Method: refined / Origin x: -25.7333 Å / Origin y: 53.053 Å / Origin z: 24.8756 Å
111213212223313233
T0.347 Å20.0211 Å20.0166 Å2-0.0939 Å2-0.0093 Å2--0.0192 Å2
L0.5641 °2-0.0857 °21.3482 °2-1.0467 °2-0.5112 °2--3.4727 °2
S0.0447 Å °0.1291 Å °0.006 Å °0.5774 Å °0.006 Å °0.0512 Å °-0.0236 Å °0.3199 Å °-0.0507 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 227
2X-RAY DIFFRACTION1A1001 - 1196
3X-RAY DIFFRACTION1A238 - 320

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