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- PDB-9xpl: Crystal structure of the pufferfish taste receptor Tas1r1-Tas1r3 ... -

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Basic information

Entry
Database: PDB / ID: 9xpl
TitleCrystal structure of the pufferfish taste receptor Tas1r1-Tas1r3 ligand binding domains in complex with D-phenylalanine
Components
  • Taste receptor type 1 member 3
  • Taste receptor, type 1, member 1
KeywordsSIGNALING PROTEIN / Taste receptor
Function / homology
Function and homology information


sensory perception of umami taste / sensory perception of sweet taste / sensory perception of taste / G protein-coupled receptor activity / plasma membrane
Similarity search - Function
GPCR, family 3, extracellular calcium-sensing receptor-related / G-protein coupled receptors family 3 signature 3. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal ...GPCR, family 3, extracellular calcium-sensing receptor-related / G-protein coupled receptors family 3 signature 3. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
D-PHENYLALANINE / Taste receptor type 1 member 3 / Taste receptor, type 1, member 1
Similarity search - Component
Biological speciesTakifugu rubripes (torafugu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMizoguchi, R. / Matsuura, H. / Hirata, K. / Yamashita, A.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H04621, JP20H04778, JP20H03195, JP23H02424, JP23K27117, JP24K21272, JP23K26861, JP25H01362 Japan
Japan Science and TechnologyJPMJFR220C Japan
Society for Research on Umami Taste Japan
Takeda Science Foundation Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Identification and structural characterization of stereochemical promiscuity in a taste receptor.
Authors: Mizoguchi, R. / Toda, Y. / Nagae, M. / Yoshida, T. / Matsuura, H. / Hirata, K. / Lam, V.T. / Tran, D.P. / Kitao, A. / Miyanoiri, Y. / Hosotani, M. / Ashikawa, Y. / Ito, C. / Tsutsumi, N. / ...Authors: Mizoguchi, R. / Toda, Y. / Nagae, M. / Yoshida, T. / Matsuura, H. / Hirata, K. / Lam, V.T. / Tran, D.P. / Kitao, A. / Miyanoiri, Y. / Hosotani, M. / Ashikawa, Y. / Ito, C. / Tsutsumi, N. / Yasui, N. / Ishimaru, Y. / Yamashita, A.
History
DepositionNov 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Taste receptor, type 1, member 1
B: Taste receptor type 1 member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,60912
Polymers112,6902
Non-polymers1,91910
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-28 kcal/mol
Surface area38600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.460, 106.900, 101.670
Angle α, β, γ (deg.)90.00, 91.91, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Taste receptor, type 1, member 1


Mass: 56288.871 Da / Num. of mol.: 1 / Mutation: C242S
Source method: isolated from a genetically manipulated source
Details: ligand-binding domain / Source: (gene. exp.) Takifugu rubripes (torafugu) / Gene: TAS1R1 / Details (production host): pAc5.1/V5-His A / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q2MHK1
#2: Protein Taste receptor type 1 member 3


Mass: 56400.965 Da / Num. of mol.: 1 / Mutation: C238S
Source method: isolated from a genetically manipulated source
Details: ligand-binding domain / Source: (gene. exp.) Takifugu rubripes (torafugu) / Gene: tas1r3 / Details (production host): pAc5.1/V5-His A / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: H2UNJ5

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Sugars , 2 types, 6 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 31 molecules

#5: Chemical ChemComp-DPN / D-PHENYLALANINE


Type: D-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antidepressant, inhibitor*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG3350, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 23572 / % possible obs: 99.6 % / Redundancy: 183 % / CC1/2: 0.991 / Rmerge(I) obs: 0.439 / Rpim(I) all: 0.03 / Rrim(I) all: 0.44 / Net I/av σ(I): 29.3 / Net I/σ(I): 29.3
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 183 % / Rmerge(I) obs: 4.04 / Mean I/σ(I) obs: 3.54 / Num. unique obs: 3865 / CC1/2: 0.492 / Rpim(I) all: 0.282 / Rrim(I) all: 4.06 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.21_5207:refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→45.25 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1204 5 %Random selection
Rwork0.2149 ---
obs-23561 99.58 %-
Refinement stepCycle: LAST / Resolution: 2.9→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7102 0 124 27 7253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037390
X-RAY DIFFRACTIONf_angle_d0.54910060
X-RAY DIFFRACTIONf_dihedral_angle_d7.5421023
X-RAY DIFFRACTIONf_chiral_restr0.0431175
X-RAY DIFFRACTIONf_plane_restr0.0041262
LS refinement shellResolution: 2.9→3.02 Å
RfactorNum. reflection% reflection
Rfree0.3284 113 5 %
Rwork0.302 2478 -
obs--99.46 %

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