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- PDB-5x2n: Crystal structure of the medaka fish taste receptor T1r2a-T1r3 li... -

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Basic information

Entry
Database: PDB / ID: 5x2n
TitleCrystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-alanine
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
ALANINE / 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: 2.2 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)310,93039
Polymers305,3698
Non-polymers5,56131
Water13,421745
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)155,57620
Polymers152,6854
Non-polymers2,89116
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)155,35419
Polymers152,6854
Non-polymers2,67015
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.372, 117.472, 130.055
Angle α, β, γ (deg.)90.00, 91.93, 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 / Cell line (production host): Schneider 2 / 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, 23 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.: 23
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 , 4 types, 753 molecules

#6: Chemical
ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
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

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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: Oct 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 145695 / % possible obs: 95.3 % / Redundancy: 3.5 % / Rsym value: 0.082 / Net I/σ(I): 18.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7359 / Rsym value: 0.58 / % possible all: 97.1

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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: 2.2→49.658 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 7095 4.92 %
Rwork0.1947 --
obs0.1971 144158 95.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→49.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20557 0 350 745 21652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821471
X-RAY DIFFRACTIONf_angle_d1.129153
X-RAY DIFFRACTIONf_dihedral_angle_d13.9237724
X-RAY DIFFRACTIONf_chiral_restr0.0423336
X-RAY DIFFRACTIONf_plane_restr0.0053684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.32662440.27094592X-RAY DIFFRACTION97
2.225-2.25120.37262430.31684620X-RAY DIFFRACTION97
2.2512-2.27860.33862420.28494641X-RAY DIFFRACTION97
2.2786-2.30750.29552650.24524635X-RAY DIFFRACTION97
2.3075-2.33780.33272480.23844588X-RAY DIFFRACTION97
2.3378-2.36990.28142560.23524607X-RAY DIFFRACTION97
2.3699-2.40370.28712450.23474635X-RAY DIFFRACTION97
2.4037-2.43960.28912590.22984627X-RAY DIFFRACTION97
2.4396-2.47770.292440.22934583X-RAY DIFFRACTION96
2.4777-2.51830.30622490.22494538X-RAY DIFFRACTION96
2.5183-2.56180.28462330.23344618X-RAY DIFFRACTION96
2.5618-2.60830.29492340.22754533X-RAY DIFFRACTION94
2.6083-2.65850.28752190.22774334X-RAY DIFFRACTION91
2.6585-2.71280.30051890.2223912X-RAY DIFFRACTION82
2.7128-2.77170.2742390.22394550X-RAY DIFFRACTION95
2.7717-2.83620.28832310.22534696X-RAY DIFFRACTION98
2.8362-2.90710.31392240.22244715X-RAY DIFFRACTION98
2.9071-2.98570.29022650.23244640X-RAY DIFFRACTION98
2.9857-3.07360.27152560.22694712X-RAY DIFFRACTION98
3.0736-3.17280.27542540.21594686X-RAY DIFFRACTION98
3.1728-3.28610.29581990.22354691X-RAY DIFFRACTION97
3.2861-3.41770.26372150.21714669X-RAY DIFFRACTION96
3.4177-3.57320.26742080.20174647X-RAY DIFFRACTION96
3.5732-3.76150.22662370.18884444X-RAY DIFFRACTION93
3.7615-3.99710.20182210.17363928X-RAY DIFFRACTION82
3.9971-4.30550.17242190.1554749X-RAY DIFFRACTION98
4.3055-4.73850.17582500.14124780X-RAY DIFFRACTION99
4.7385-5.42350.19862340.14464650X-RAY DIFFRACTION97
5.4235-6.83020.20832470.17134560X-RAY DIFFRACTION94
6.8302-49.67030.2132260.16464483X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 90.8622 Å / Origin y: 51.6828 Å / Origin z: 31.8278 Å
111213212223313233
T0.3418 Å20.0035 Å20.009 Å2-0.3704 Å20.0009 Å2--0.2993 Å2
L0.1855 °20.0466 °20.0518 °2-0.0688 °20.0396 °2--0.0103 °2
S0.0038 Å °-0.0524 Å °0.0129 Å °-0.0179 Å °-0.0208 Å °0.0149 Å °-0.0263 Å °0.0216 Å °0.0144 Å °
Refinement TLS groupSelection details: ALL

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