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- PDB-5x2q: Crystal structure of the medaka fish taste receptor T1r2a-T1r3 li... -

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Basic information

Entry
Database: PDB / ID: 5x2q
TitleCrystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with glycine
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
GLYCINE / 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_label_asym_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Nov 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 2.2Oct 9, 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)311,58744
Polymers305,3698
Non-polymers6,21836
Water7,332407
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)156,15722
Polymers152,6854
Non-polymers3,47318
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)155,43022
Polymers152,6854
Non-polymers2,74518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.517, 112.724, 128.685
Angle α, β, γ (deg.)90.00, 92.16, 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 , 3 types, 23 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: 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.: 21
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, 420 molecules

#8: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#9: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
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: Jan 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: 84819 / % possible obs: 98 % / Redundancy: 3 % / Rsym value: 0.091 / Net I/σ(I): 10.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4175 / Rsym value: 0.391 / % possible all: 97.2

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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→49.276 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.66
RfactorNum. reflection% reflection
Rfree0.2297 4248 5.01 %
Rwork0.1535 --
obs0.1573 84789 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.21 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20467 0 390 407 21264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221416
X-RAY DIFFRACTIONf_angle_d1.23629089
X-RAY DIFFRACTIONf_dihedral_angle_d14.2297716
X-RAY DIFFRACTIONf_chiral_restr0.0493344
X-RAY DIFFRACTIONf_plane_restr0.0063683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5988-2.62830.30091420.19862579X-RAY DIFFRACTION93
2.6283-2.65920.28081500.19242518X-RAY DIFFRACTION95
2.6592-2.69160.2991170.19542484X-RAY DIFFRACTION92
2.6916-2.72570.27181430.18322644X-RAY DIFFRACTION96
2.7257-2.76160.29771430.18442727X-RAY DIFFRACTION99
2.7616-2.79940.28161390.17732671X-RAY DIFFRACTION99
2.7994-2.83940.23141470.17442689X-RAY DIFFRACTION99
2.8394-2.88180.27131440.17672720X-RAY DIFFRACTION99
2.8818-2.92680.25891230.18082720X-RAY DIFFRACTION99
2.9268-2.97480.30191400.19072705X-RAY DIFFRACTION99
2.9748-3.0260.28311390.17912694X-RAY DIFFRACTION99
3.026-3.08110.26831640.17722696X-RAY DIFFRACTION99
3.0811-3.14030.25091370.16582736X-RAY DIFFRACTION99
3.1403-3.20440.27871320.16582741X-RAY DIFFRACTION99
3.2044-3.27410.24621610.16472681X-RAY DIFFRACTION99
3.2741-3.35020.25581240.16392731X-RAY DIFFRACTION99
3.3502-3.4340.25011270.16192712X-RAY DIFFRACTION99
3.434-3.52680.25341560.15582704X-RAY DIFFRACTION99
3.5268-3.63050.23781410.14882741X-RAY DIFFRACTION99
3.6305-3.74770.1991520.14992652X-RAY DIFFRACTION98
3.7477-3.88160.23191350.14442594X-RAY DIFFRACTION94
3.8816-4.03690.21431140.14722602X-RAY DIFFRACTION94
4.0369-4.22060.19631440.13062719X-RAY DIFFRACTION99
4.2206-4.44290.19571510.12362742X-RAY DIFFRACTION99
4.4429-4.72110.15811540.11732725X-RAY DIFFRACTION99
4.7211-5.08530.17141410.12392715X-RAY DIFFRACTION99
5.0853-5.59640.19961400.13762747X-RAY DIFFRACTION99
5.5964-6.40470.23951380.15982714X-RAY DIFFRACTION98
6.4047-8.06350.21171480.16472618X-RAY DIFFRACTION94
8.0635-49.28480.22061620.14372820X-RAY DIFFRACTION100
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)
11.0738-0.5696-0.20221.41160.75161.00670.002-0.0247-0.043-0.00720.03790.0113-0.0468-0.0157-0.0360.1813-0.00480.00560.19120.04670.17645.769630.183340.2326
22.3162-0.6322-0.80570.64170.35812.04260.02090.1123-0.0128-0.0804-0.0404-0.17570.02490.46140.01480.27690.05390.01850.34790.02590.244246.800139.94265.4308
30.95780.67010.03111.08220.22291.08180.0296-0.0010.08080.01830.0390.04110.02120.037-0.06050.16040.02070.00040.1551-0.00530.1891100.191370.940622.0714
41.36150.01750.74280.92210.28582.4551-0.07350.03570.0420.01680.1048-0.1544-0.12750.2839-0.02340.24260.00990.02150.17930.01140.194897.712563.545156.8665
51.5023-0.2637-0.66670.9621-0.19750.76450.0367-0.06530.24980.0553-0.0438-0.2421-0.13120.14870.00480.2718-0.0067-0.04980.2267-0.01170.331299.411513.759728.9209
61.62560.0633-0.23390.4292-0.07880.6196-0.00830.09750.03520.0066-0.0407-0.08490.02570.12590.04160.24970.0123-0.02090.22080.02310.2229101.7873-0.035317.3056
72.1703-0.33150.4410.41640.10460.48350.00860.1674-0.08540.0322-0.0068-0.01490.10670.008-0.00780.2591-0.01740.00930.24020.00750.2444152.036187.457336.8217
81.42890.10850.3340.18540.01260.1488-0.0236-0.07840.0410.01770.01630.02060.0176-0.06580.01320.2248-0.02380.00560.22370.01430.2164154.6626100.54249.4492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 466 )
2X-RAY DIFFRACTION2chain 'B' and (resid 21 through 470 )
3X-RAY DIFFRACTION3chain 'C' and (resid 25 through 465 )
4X-RAY DIFFRACTION4chain 'D' and (resid 21 through 470 )
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 224 )
6X-RAY DIFFRACTION6chain 'L' and (resid 1 through 217 )
7X-RAY DIFFRACTION7chain 'J' and (resid 1 through 225 )
8X-RAY DIFFRACTION8chain 'K' and (resid 1 through 216 )

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