[English] 日本語
Yorodumi
- EMDB-70737: Structure of the sweet receptor bound to advantame in the loose s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70737
TitleStructure of the sweet receptor bound to advantame in the loose state, extracellular domain
Map data
Sample
  • Complex: Human TAS1R2 and mouse TAS1R3 sweet receptor bound to advantame
    • Complex: TAS1R2
      • Protein or peptide: Taste receptor type 1 member 2
    • Complex: TAS1R3
      • Protein or peptide: Taste receptor type 1 member 3
  • Ligand: advantame
KeywordsMembrane protein / GPCR / SIGNALING PROTEIN
Function / homology
Function and homology information


Class C/3 (Metabotropic glutamate/pheromone receptors) / Sensory perception of sweet, bitter, and umami (glutamate) taste / sweet taste receptor complex / detection of chemical stimulus involved in sensory perception of sweet taste / sweet taste receptor activity / taste receptor activity / sensory perception of umami taste / G alpha (i) signalling events / sensory perception of sweet taste / Class C/3 (Metabotropic glutamate/pheromone receptors) ...Class C/3 (Metabotropic glutamate/pheromone receptors) / Sensory perception of sweet, bitter, and umami (glutamate) taste / sweet taste receptor complex / detection of chemical stimulus involved in sensory perception of sweet taste / sweet taste receptor activity / taste receptor activity / sensory perception of umami taste / G alpha (i) signalling events / sensory perception of sweet taste / Class C/3 (Metabotropic glutamate/pheromone receptors) / positive regulation of cytokinesis / G protein-coupled receptor activity / Sensory perception of sweet, bitter, and umami (glutamate) taste / G alpha (i) signalling events / receptor complex / G protein-coupled receptor signaling pathway / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
GPCR, family 3, extracellular calcium-sensing receptor-related / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR ...GPCR, family 3, extracellular calcium-sensing receptor-related / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / 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
Similarity search - Domain/homology
Taste receptor type 1 member 2 / Taste receptor type 1 member 3
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsWang H / Chen X / Dai Y / Lee CH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143282 United States
CitationJournal: To Be Published
Title: Structure of the sweet receptor bound to advantame in the loose state, extracellular domain
Authors: Wang H / Chen X / Dai Y / Lee CH
History
DepositionMay 20, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70737.png

Downloads & links

-
Map

FileDownload / File: emd_70737.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 216 pix.
= 311.515 Å		1.44 Å/pix.
x 216 pix.
= 311.515 Å		1.44 Å/pix.
x 216 pix.
= 311.515 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4422 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.02
Minimum - Maximum-4.3519 - 7.36519
Average (Standard dev.)0.004946259 (±0.14124367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 311.5152 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_70737_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_70737_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human TAS1R2 and mouse TAS1R3 sweet receptor bound to advantame

EntireName: Human TAS1R2 and mouse TAS1R3 sweet receptor bound to advantame
Components
  • Complex: Human TAS1R2 and mouse TAS1R3 sweet receptor bound to advantame
    • Complex: TAS1R2
      • Protein or peptide: Taste receptor type 1 member 2
    • Complex: TAS1R3
      • Protein or peptide: Taste receptor type 1 member 3
  • Ligand: advantame

-
Supramolecule #1: Human TAS1R2 and mouse TAS1R3 sweet receptor bound to advantame

SupramoleculeName: Human TAS1R2 and mouse TAS1R3 sweet receptor bound to advantame
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

-
Supramolecule #2: TAS1R2

SupramoleculeName: TAS1R2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: TAS1R3

SupramoleculeName: TAS1R3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Taste receptor type 1 member 2

MacromoleculeName: Taste receptor type 1 member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.842008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENSDFYLPG DYLLGGLFSL HANMKGIVHL NFLQVPMCKE YEVKVIGYNL MQAMRFAVEE INNDSSLLPG VLLGYEIVDV CYISNNVQP VLYFLAHEDN LLPIQEDYSN YSSRVVAVIG PDNSESVMTV ANFLSLFLLP QITYSAISDE LRDKVRFPAL L RTTPSADH ...String:
AENSDFYLPG DYLLGGLFSL HANMKGIVHL NFLQVPMCKE YEVKVIGYNL MQAMRFAVEE INNDSSLLPG VLLGYEIVDV CYISNNVQP VLYFLAHEDN LLPIQEDYSN YSSRVVAVIG PDNSESVMTV ANFLSLFLLP QITYSAISDE LRDKVRFPAL L RTTPSADH HIEAMVQLML HFRWNWIIVL VSNDTYGRDN GQLLGERVAR RGICIAFQET LPTLQPNQNM TSEERQRLVT IV DKLQQST ARVVVVFSPD LTLYHFFNEV LRQNFTGAVW IASESWAIDP VLHNLTELRH LGTFLGITIQ SVPIPGFSEF REW GPQAGP PPLSRTSQSY TCNQECDNCL NATLSFNTIL RLSGERVVYS VYSAVYAVAH ALHSLLGCDK STCTKRVVYP WQLL EEIWK VNFTLLDHQI FFDPQGDVAL HLEIVQWQWD RSQNPFQSVA SYYPLQRQLK NIQDISWHTI NNTIPMSMCS KRCQS GQKK KPVGIHVCCF ECIDCLPGTF LNHTEDEYEC QACPNNEWSY QSETSCFKRQ LVFLEWHEAP TIAVALLAAL GFLSTL AIL VIFWRHFQTP IVRSAGGPMC FLMLTLLLVA YMVVPVYVGP PKVSTCLCRQ ALFPLCFTIC ISCIAVRSFQ IVCAFKM AS RFPRAYSYWV RYQGPYVSMA FITVLKMVIV VIGMLATGLS PTTRTDPDDP KITIVSCNPN YRNSLLFNTS LDLLLSVV G FSFAYMGKEL PTNYNEAKFI TLSMTFYFTS SVSLCTFMSA YSGVLVTIVD LLVTVLNLLA ISLGYFGPKC YMILFYPER NTPAYFNSMI QGYTMRRD

UniProtKB: Taste receptor type 1 member 2

-
Macromolecule #2: Taste receptor type 1 member 3

MacromoleculeName: Taste receptor type 1 member 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 92.648562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ASLCLSQQFK AQGDYILGGL FPLGSTEEAT LNQRTQPNSI PCNRFSPLGL FLAMAMKMAV EEINNGSALL PGLRLGYDLF DTCSEPVVT MKSSLMFLAK VGSQSIAAYC NYTQYQPRVL AVIGPHSSEL ALITGKFFSF FLMPQVSYSA SMDRLSDRET F PSFFRTVP ...String:
ASLCLSQQFK AQGDYILGGL FPLGSTEEAT LNQRTQPNSI PCNRFSPLGL FLAMAMKMAV EEINNGSALL PGLRLGYDLF DTCSEPVVT MKSSLMFLAK VGSQSIAAYC NYTQYQPRVL AVIGPHSSEL ALITGKFFSF FLMPQVSYSA SMDRLSDRET F PSFFRTVP SDRVQLQAVV TLLQNFSWNW VAALGSDDDY GREGLSIFSS LANARGICIA HEGLVPQHDT SGQQLGKVLD VL RQVNQSK VQVVVLFASA RAVYSLFSYS IHHGLSPKVW VASESWLTSD LVMTLPNIAR VGTVLGFLQR GALLPEFSHY VET HLALAA DPAFCASLNA ELDLEEHVMG QRCPRCDDIM LQNLSSGLLQ NLSAGQLHHQ IFATYAAVYS VAQALHNTLQ CNVS HCHVS EHVLPWQLLE NMYNMSFHAR DLTLQFDAEG NVDMEYDLKM WVWQSPTPVL HTVGTFNGTL QLQQSKMYWP GNQVP VSQC SRQCKDGQVR RVKGFHSCCY DCVDCKAGSY RKHPDDFTCT PCNQDQWSPE KSTACLPRRP KFLAWGEPVV LSLLLL LCL VLGLALAALG LSVHHWDSPL VQASGGSQFC FGLICLGLFC LSVLLFPGRP SSASCLAQQP MAHLPLTGCL STLFLQA AE TFVESELPLS WANWLCSYLR GLWAWLVVLL ATFVEAALCA WYLIAFPPEV VTDWSVLPTE VLEHCHVRSW VSLGLVHI T NAMLAFLCFL GTFLVQSQPG RYNRARGLTF AMLAYFITWV SFVPLLANVQ VAYQPAVQMG AILVCALGIL VTFHLPKCY VLLWLPKLNT QEFFLGRNAK KAADENSGGG EAAQGHNE

UniProtKB: Taste receptor type 1 member 3

-
Macromolecule #3: advantame

MacromoleculeName: advantame / type: ligand / ID: 3 / Number of copies: 1 / Formula: A1CD7
Molecular weightTheoretical: 458.504 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146192
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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