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- PDB-5x2p: Crystal structure of the medaka fish taste receptor T1r2a-T1r3 li... -

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Basic information

Entry
Database: PDB / ID: 5x2p
TitleCrystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-glutamate
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
GLUTAMIC ACID / 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: 2.608 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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 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)312,21342
Polymers305,3698
Non-polymers6,84434
Water7,512417
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)156,49922
Polymers152,6854
Non-polymers3,81518
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)155,71420
Polymers152,6854
Non-polymers3,02916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.632, 116.063, 129.592
Angle α, β, γ (deg.)90.00, 91.56, 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, 25 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.: 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 , 5 types, 426 molecules

#8: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
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, 100 mM L-Glu

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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 27, 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: 86102 / % possible obs: 96.1 % / Redundancy: 3.1 % / Rsym value: 0.104 / Net I/σ(I): 3.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4273 / Rsym value: 0.5 / % possible all: 95.9

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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: 2.608→50 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.13
RfactorNum. reflection% reflection
Rfree0.2283 4295 4.99 %
Rwork0.1531 --
obs0.1569 86074 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.25 Å2
Refinement stepCycle: LAST / Resolution: 2.608→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20215 0 434 417 21066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921196
X-RAY DIFFRACTIONf_angle_d1.20828810
X-RAY DIFFRACTIONf_dihedral_angle_d14.6927645
X-RAY DIFFRACTIONf_chiral_restr0.0463320
X-RAY DIFFRACTIONf_plane_restr0.0053648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.608-2.63760.33051170.2282447X-RAY DIFFRACTION85
2.6376-2.66870.28111450.21242647X-RAY DIFFRACTION96
2.6687-2.70120.29821210.20832763X-RAY DIFFRACTION96
2.7012-2.73540.27431430.19192702X-RAY DIFFRACTION96
2.7354-2.77140.31091290.18912796X-RAY DIFFRACTION96
2.7714-2.80930.26951380.18662692X-RAY DIFFRACTION95
2.8093-2.84950.29081360.18712606X-RAY DIFFRACTION92
2.8495-2.8920.28431290.19182470X-RAY DIFFRACTION88
2.892-2.93720.28661550.18582772X-RAY DIFFRACTION97
2.9372-2.98530.29411440.18592753X-RAY DIFFRACTION98
2.9853-3.03680.28071570.18372741X-RAY DIFFRACTION97
3.0368-3.0920.26721560.18942764X-RAY DIFFRACTION98
3.092-3.15150.27251350.17742801X-RAY DIFFRACTION98
3.1515-3.21580.24831330.17062778X-RAY DIFFRACTION97
3.2158-3.28570.27041380.17462731X-RAY DIFFRACTION97
3.2857-3.36210.25791490.172798X-RAY DIFFRACTION98
3.3621-3.44620.25071500.16762776X-RAY DIFFRACTION98
3.4462-3.53930.26591350.16372793X-RAY DIFFRACTION98
3.5393-3.64350.23321610.15012715X-RAY DIFFRACTION97
3.6435-3.7610.21321590.14312469X-RAY DIFFRACTION88
3.761-3.89540.23091370.13492781X-RAY DIFFRACTION97
3.8954-4.05130.20261470.13112823X-RAY DIFFRACTION99
4.0513-4.23560.17981360.12222827X-RAY DIFFRACTION99
4.2356-4.45880.17831400.11632832X-RAY DIFFRACTION99
4.4588-4.73790.16281550.10812780X-RAY DIFFRACTION98
4.7379-5.10340.18091590.11322756X-RAY DIFFRACTION97
5.1034-5.61640.20511450.12612585X-RAY DIFFRACTION90
5.6164-6.42760.19361410.14622833X-RAY DIFFRACTION98
6.4276-8.09260.20891560.15832793X-RAY DIFFRACTION97
8.0926-50.150.20711490.15652755X-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)
11.4661-0.9047-0.37642.16670.85041.1454-0.0564-0.0826-0.14650.07570.03660.0701-0.0112-0.05520.01260.1695-0.0111-00.22710.0630.178746.880830.37441.0837
23.544-0.7427-1.19990.90070.34322.22210.18150.34150.0367-0.1544-0.1446-0.0975-0.2782-0.0998-0.01590.33770.0374-0.00010.12680.02360.212447.167540.65365.7532
30.97680.6179-0.02131.77780.28791.10890.00610.06280.0815-0.0457-0.02720.1984-0.047-0.10390.02050.14590.0029-0.01420.24770.00140.1983101.962274.00322.0679
42.2260.0520.30412.0654-0.73644.4149-0.0011-0.55540.12250.2664-0.1593-0.2522-0.41350.32790.13930.2928-0.0295-0.00570.4817-0.04390.249598.358463.523857.0486
53.7364-0.3843-1.1581.1305-0.05370.7730.1195-0.15360.47680.0074-0.0926-0.2898-0.12310.1969-0.02540.2402-0.0194-0.05610.20160.0160.3122100.385414.17929.1489
62.8539-0.1996-0.27760.6176-0.18020.77810.0610.21150.0136-0.0082-0.1256-0.13240.05850.12710.07820.23920.0082-0.03340.16840.03810.1778103.08110.498417.3348
74.14250.22091.610.70030.37880.63950.01820.4151-0.24040.05640.0521-0.08440.15420.1902-0.0770.3018-0.03510.09370.2856-0.0170.2559153.979390.532736.5417
83.9999-0.090.59460.45920.18290.5244-0.115-0.09120.02710.01290.0789-0.02680.05760.04820.03180.266-0.01250.04120.17970.01930.2163156.7784103.472349.4903
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 471 )
3X-RAY DIFFRACTION3chain 'C' and (resid 25 through 465 )
4X-RAY DIFFRACTION4chain 'D' and (resid 20 through 474 )
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 224 )
8X-RAY DIFFRACTION8chain 'K' and (resid 1 through 216 )

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