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- PDB-5x2o: Crystal structure of the medaka fish taste receptor T1r2a-T1r3 li... -

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Entry
Database: PDB / ID: 5x2o
TitleCrystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-arginine
Components
  • (Taste receptor, type 1, member ...) x 2
  • Fab16A Heavy chain
  • Fab16A Light chain
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / receptor / ligand binding / amino acid / venus-flytrap domain / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


G protein-coupled receptor activity / plasma membrane
Similarity search - Function
GPCR, family 3, extracellular calcium-sensing receptor-related / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / 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 ...GPCR, family 3, extracellular calcium-sensing receptor-related / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ARGININE / Taste receptor type 1 member 3 / Taste receptor, type 1, member 2a
Similarity search - Component
Biological speciesOryzias latipes (Japanese medaka)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNuemket, N. / Yasui, N. / Atsumi, N. / Yamashita, A.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for perception of diverse chemical substances by T1r taste receptors
Authors: Nuemket, N. / Yasui, N. / Kusakabe, Y. / Nomura, Y. / Atsumi, N. / Akiyama, S. / Nango, E. / Kato, Y. / Kaneko, M.K. / Takagi, J. / Hosotani, M. / Yamashita, A.
History
DepositionFeb 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Taste receptor, type 1, member 2a
B: Taste receptor, type 1, member 3
C: Taste receptor, type 1, member 2a
D: Taste receptor, type 1, member 3
H: Fab16A Heavy chain
L: Fab16A Light chain
J: Fab16A Heavy chain
K: Fab16A Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,04746
Polymers305,3698
Non-polymers6,67838
Water6,539363
1
A: Taste receptor, type 1, member 2a
B: Taste receptor, type 1, member 3
H: Fab16A Heavy chain
L: Fab16A Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,21323
Polymers152,6854
Non-polymers3,52919
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Taste receptor, type 1, member 2a
D: Taste receptor, type 1, member 3
J: Fab16A Heavy chain
K: Fab16A Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,83423
Polymers152,6854
Non-polymers3,14919
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.905, 113.677, 128.636
Angle α, β, γ (deg.)90.00, 92.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Taste receptor, type 1, member ... , 2 types, 4 molecules ACBD

#1: Protein Taste receptor, type 1, member 2a / T1r2a


Mass: 51471.105 Da / Num. of mol.: 2 / Fragment: UNP residues 12-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryzias latipes (Japanese medaka) / Gene: TAS1R2a / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A173M0G2
#2: Protein Taste receptor, type 1, member 3 / T1r3


Mass: 53131.977 Da / Num. of mol.: 2 / Fragment: UNP residues 12-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryzias latipes (Japanese medaka) / Gene: TAS1R3 / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A173M094

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Antibody , 2 types, 4 molecules HJLK

#3: Antibody Fab16A Heavy chain


Mass: 24182.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Antibody Fab16A Light chain


Mass: 23899.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Sugars , 1 types, 26 molecules

#5: 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.: 26
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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 , 5 types, 375 molecules

#6: Chemical
ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N4O2
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 12~13% (w/v) PEG 1500, 3% (v/v) PEG400, 0.1 M MES, L-Arginine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2015
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: 84573 / % possible obs: 95.9 % / Redundancy: 2.8 % / Rsym value: 0.125 / Net I/σ(I): 11.9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4128 / Rsym value: 0.38 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E4U, 1A6T

2e4u

1a6t


Resolution: 2.6→49.415 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.32
RfactorNum. reflection% reflection
Rfree0.2715 4231 5.01 %
Rwork0.1847 --
obs0.189 84535 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.14 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20363 0 420 363 21146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01121353
X-RAY DIFFRACTIONf_angle_d1.22429013
X-RAY DIFFRACTIONf_dihedral_angle_d14.8117700
X-RAY DIFFRACTIONf_chiral_restr0.0463341
X-RAY DIFFRACTIONf_plane_restr0.0053671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5904-2.61990.3751230.23732238X-RAY DIFFRACTION81
2.6199-2.65070.30151550.22032622X-RAY DIFFRACTION94
2.6507-2.6830.33121320.21552685X-RAY DIFFRACTION95
2.683-2.7170.29971200.21152624X-RAY DIFFRACTION94
2.717-2.75270.33011490.2082676X-RAY DIFFRACTION95
2.7527-2.79040.33451440.21482615X-RAY DIFFRACTION94
2.7904-2.83030.331370.20832498X-RAY DIFFRACTION90
2.8303-2.87250.33921410.21232494X-RAY DIFFRACTION91
2.8725-2.91740.31161500.21652720X-RAY DIFFRACTION96
2.9174-2.96520.35011580.21722707X-RAY DIFFRACTION98
2.9652-3.01640.3361450.20362702X-RAY DIFFRACTION98
3.0164-3.07120.31021420.21212762X-RAY DIFFRACTION98
3.0712-3.13030.30691430.19652747X-RAY DIFFRACTION99
3.1303-3.19420.30341130.20332777X-RAY DIFFRACTION98
3.1942-3.26360.30851310.20242768X-RAY DIFFRACTION98
3.2636-3.33950.3071430.20182739X-RAY DIFFRACTION98
3.3395-3.4230.28821330.22742X-RAY DIFFRACTION98
3.423-3.51550.31221380.19382714X-RAY DIFFRACTION97
3.5155-3.61890.25091320.18742668X-RAY DIFFRACTION96
3.6189-3.73570.28651430.18192538X-RAY DIFFRACTION91
3.7357-3.86920.26661600.17882694X-RAY DIFFRACTION96
3.8692-4.0240.22721480.17712773X-RAY DIFFRACTION99
4.024-4.20710.24741230.16182783X-RAY DIFFRACTION99
4.2071-4.42870.2341590.1572741X-RAY DIFFRACTION98
4.4287-4.7060.24291420.15522723X-RAY DIFFRACTION97
4.706-5.0690.24021370.15582736X-RAY DIFFRACTION97
5.069-5.57850.24521540.17122570X-RAY DIFFRACTION91
5.5785-6.38430.26761390.1892750X-RAY DIFFRACTION97
6.3843-8.03790.24761590.18112764X-RAY DIFFRACTION97
8.0379-49.42390.18341380.16352734X-RAY DIFFRACTION94
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)
11.4515-0.9599-0.26851.56050.68520.9133-0.0458-0.0906-0.12160.04030.04620.0528-0.0032-0.161-0.00320.2412-0.022-0.01370.26940.06780.21245.903829.962140.2393
22.892-0.4788-1.15561.03950.61292.22380.10470.3533-0.03-0.2565-0.1999-0.169-0.15430.26620.09440.37290.08150.02590.4610.09990.287147.159940.41155.5854
31.34810.88340.11462.06350.43771.14160.02550.04030.0789-0.01670.04530.07520.0040.0545-0.0730.17950.03320.00180.22860.00760.1992100.66772.004322.1218
41.9756-0.05040.92911.56530.28763.41-0.10920.01990.12190.06450.1639-0.2245-0.29310.4313-0.05290.3575-0.01740.03560.2802-0.01540.229297.854963.743256.9561
52.9791-0.4383-1.12891.0906-0.17881.29010.0816-0.17320.26290.0966-0.1132-0.3222-0.22960.36970.04830.2931-0.0396-0.0940.29130.04310.338699.667813.989929.2762
62.93680.2979-0.13571.0503-0.47840.84060.02560.2767-0.040.0023-0.1156-0.19850.00910.30140.09470.2850.0116-0.02380.310.01510.2023102.04860.348417.5798
73.8277-0.37211.13750.66240.08290.67490.09640.304-0.09390.0518-0.0402-0.06180.14560.0573-0.04410.3104-0.05870.03690.2431-0.01650.2454152.828488.239636.9304
82.91240.00760.54190.256-0.0610.2826-0.0258-0.23230.0458-0.00120.04810.02740.0543-0.0644-0.01670.2564-0.01520.02450.2643-0.00380.2373155.2446101.296149.4349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 466 )
2X-RAY DIFFRACTION2chain 'B' and (resid 21 through 490 )
3X-RAY DIFFRACTION3chain 'C' and (resid 25 through 465 )
4X-RAY DIFFRACTION4chain 'D' and (resid 20 through 486 )
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 224 )
6X-RAY DIFFRACTION6chain 'L' and (resid 1 through 216 )
7X-RAY DIFFRACTION7chain 'J' and (resid 1 through 225 )
8X-RAY DIFFRACTION8chain 'K' and (resid 1 through 216 )

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