[English] 日本語
Yorodumi
- PDB-5x2m: Crystal structure of the medaka fish taste receptor T1r2a-T1r3 li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x2m
TitleCrystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-glutamine
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
GLUTAMINE / 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: 2.206 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.ptnr1_symmetry / _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_label_seq_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)312,10645
Polymers305,3698
Non-polymers6,73737
Water13,962775
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)156,17223
Polymers152,6854
Non-polymers3,48819
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)155,93422
Polymers152,6854
Non-polymers3,24918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.656, 116.355, 129.476
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
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

-
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)

-
Sugars , 1 types, 27 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.: 27
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

-
Non-polymers , 5 types, 785 molecules

#6: Chemical
ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10N2O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / 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.: 775 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.93 %
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, 5 mM Glutamine

-
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 5, 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: 142788 / % possible obs: 97.1 % / Redundancy: 3.3 % / Rsym value: 0.078 / Net I/σ(I): 15.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7093 / Rsym value: 0.705 / % possible all: 96.2

-
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: 2.206→49.891 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 7131 5.01 %
Rwork0.1731 --
obs0.1758 142472 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.206→49.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20290 0 424 775 21489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921295
X-RAY DIFFRACTIONf_angle_d1.15828940
X-RAY DIFFRACTIONf_dihedral_angle_d14.0237698
X-RAY DIFFRACTIONf_chiral_restr0.0463335
X-RAY DIFFRACTIONf_plane_restr0.0053664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.206-2.23110.36561710.30233318X-RAY DIFFRACTION71
2.2311-2.25730.39432220.36054157X-RAY DIFFRACTION89
2.2573-2.28490.3572270.28714541X-RAY DIFFRACTION97
2.2849-2.31380.29792800.22424513X-RAY DIFFRACTION97
2.3138-2.34420.27672180.2184327X-RAY DIFFRACTION93
2.3442-2.37630.2871970.21294443X-RAY DIFFRACTION94
2.3763-2.41030.28192610.20924558X-RAY DIFFRACTION98
2.4103-2.44630.29862430.21034632X-RAY DIFFRACTION98
2.4463-2.48450.24722410.19854658X-RAY DIFFRACTION99
2.4845-2.52520.27872240.19194589X-RAY DIFFRACTION98
2.5252-2.56880.26772600.18814582X-RAY DIFFRACTION98
2.5688-2.61550.25932440.19784585X-RAY DIFFRACTION98
2.6155-2.66580.29232210.19664610X-RAY DIFFRACTION98
2.6658-2.72020.28862370.20594656X-RAY DIFFRACTION98
2.7202-2.77930.26492540.20434611X-RAY DIFFRACTION98
2.7793-2.8440.27462180.19824466X-RAY DIFFRACTION95
2.844-2.91510.27232510.20644376X-RAY DIFFRACTION94
2.9151-2.99390.3112430.21384606X-RAY DIFFRACTION99
2.9939-3.0820.26432460.20274620X-RAY DIFFRACTION98
3.082-3.18140.25872480.19084589X-RAY DIFFRACTION98
3.1814-3.29510.26222230.19874658X-RAY DIFFRACTION98
3.2951-3.4270.26082470.19374616X-RAY DIFFRACTION98
3.427-3.5830.24852450.18174600X-RAY DIFFRACTION98
3.583-3.77180.21182430.16744275X-RAY DIFFRACTION91
3.7718-4.0080.18972530.14784641X-RAY DIFFRACTION98
4.008-4.31730.18112640.12984653X-RAY DIFFRACTION99
4.3173-4.75150.16142440.11544638X-RAY DIFFRACTION98
4.7515-5.43830.15872490.12164570X-RAY DIFFRACTION97
5.4383-6.84890.18432430.14994566X-RAY DIFFRACTION96
6.8489-49.90410.17462140.15194687X-RAY DIFFRACTION96
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)
11.0678-0.4395-0.10061.45570.48930.93790.001-0.0772-0.06290.02710.02630.0092-0.0584-0.0568-0.02470.2262-0.0185-0.00180.28670.0620.236746.396830.140.6005
22.4776-0.6012-1.20061.14950.57692.54950.25870.30020.1341-0.2751-0.1547-0.142-0.3986-0.1594-0.02610.42730.04620.01590.19990.05520.297547.231940.73455.6886
31.16090.6049-0.13281.26330.27171.340.01670.03090.1139-0.1096-0.00910.125-0.0461-0.1016-0.00580.3114-0.0029-0.02630.29810.03550.3126101.850474.490922.085
41.8479-0.0965-0.00641.4877-0.53174.024-0.0729-0.45530.10260.2132-0.0434-0.1905-0.2690.58150.07180.3226-0.0555-0.01310.5626-0.02380.32798.377664.74457.1466
52.67310.3598-1.50730.8274-0.3710.95460.0264-0.28460.0860.0268-0.1056-0.1221-0.08770.36620.10410.3078-0.0424-0.07630.40020.03110.2983100.227914.397929.519
61.52510.4819-0.32720.8704-0.23820.57510.0547-0.0072-0.19230.024-0.1476-0.28370.03680.23810.06920.2880.0139-0.04520.32850.06020.3557103.18290.772817.7587
73.6781-0.20691.52830.26460.11710.7512-0.01260.5331-0.2998-0.06170.0524-0.04550.08880.2139-0.0490.4461-0.0770.0960.3799-0.04840.3954153.807890.721736.6168
83.27040.14660.61840.33620.20060.3861-0.12580.01360.0107-0.0750.0716-0.03330.03320.0720.04260.3655-0.03870.0560.29280.03120.3197156.5382103.593249.5911
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 21 through 488 )
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more