[English] 日本語
Yorodumi
- PDB-9utc: The VFT domains of human sweet taste receptor TAS1R2 and TAS1R3 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9utc
TitleThe VFT domains of human sweet taste receptor TAS1R2 and TAS1R3 in the sucralose-bound state
Components
  • Taste receptor type 1 member 2,Taste receptor type 1 member 2,Engineered red fluorescent protein mScarlet3
  • Taste receptor type 1 member 3,mNeonGreen
KeywordsSIGNALING PROTEIN / GPCR / Taste receptor / Tas1R2 / Tas1R3 / Sucralose
Function / homology
Function and homology information


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 / sensory perception of sweet taste / Class C/3 (Metabotropic glutamate/pheromone receptors) / positive regulation of cytokinesis / bioluminescence / G protein-coupled receptor activity ...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 / sensory perception of sweet taste / Class C/3 (Metabotropic glutamate/pheromone receptors) / positive regulation of cytokinesis / bioluminescence / 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 / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
sucralose / mNeonGreen / Taste receptor type 1 member 3 / Taste receptor type 1 member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Discosoma sp. (sea anemone)
Branchiostoma lanceolatum (amphioxus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsShi, Z.J. / Xu, W.X. / Yue, X.L. / Wu, L.J. / Hua, T. / Liu, Z.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2025
Title: Structural and functional characterization of human sweet taste receptor.
Authors: Zongjun Shi / Weixiu Xu / Lijie Wu / Xiaolei Yue / Shenhui Liu / Wei Ding / Jinyi Zhang / Bing Meng / Lianghao Zhao / Xiaoyan Liu / Junlin Liu / Zhi-Jie Liu / Tian Hua /
Abstract: Sweet taste perception influences dietary choices and metabolic health. The human sweet taste receptor, a class C G-protein-coupled receptor (GPCR) heterodimer composed of TAS1R2 and TAS1R3 (refs. ), ...Sweet taste perception influences dietary choices and metabolic health. The human sweet taste receptor, a class C G-protein-coupled receptor (GPCR) heterodimer composed of TAS1R2 and TAS1R3 (refs. ), senses a wide range of sweet compounds-including natural sugars, artificial sweeteners and sweet proteins-and affects metabolic regulation beyond taste. However, the lack of three-dimensional structures hinders our understanding of its precise working mechanism. Here we present cryo-electron microscopy structures of the full-length human sweet taste receptor in apo and sucralose-bound states. These structures reveal a distinct asymmetric heterodimer architecture, with sucralose binding exclusively to the Venus flytrap domain of TAS1R2. Combining mutagenesis and molecular dynamics simulations, this work delineates the sweetener-recognition modes in TAS1R2. Structural comparisons further uncover conformational changes upon ligand binding and a unique activation mechanism. These findings illuminate the signal transduction mechanisms of chemosensory receptors in the class C GPCR family and provide the molecular basis for the design of a new generation of sweeteners.
History
DepositionMay 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Taste receptor type 1 member 2,Taste receptor type 1 member 2,Engineered red fluorescent protein mScarlet3
B: Taste receptor type 1 member 3,mNeonGreen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,4953
Polymers247,0982
Non-polymers3981
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Taste receptor type 1 member 2,Taste receptor type 1 member 2,Engineered red fluorescent protein mScarlet3 / G-protein coupled receptor 71 / Sweet taste receptor T1R2


Mass: 122191.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Engineered red fluorescent protein mScarlet3: PMID: 27869816 and PDB ID: 7ZCT
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Discosoma sp. (sea anemone)
Gene: TAS1R2, GPR71, T1R2, TR2 / Production host: Homo sapiens (human) / References: UniProt: Q8TE23
#2: Protein Taste receptor type 1 member 3,mNeonGreen / Sweet taste receptor T1R3


Mass: 124906.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Branchiostoma lanceolatum (amphioxus)
Gene: TAS1R3, T1R3, TR3, blFP-Y3 / Production host: Homo sapiens (human) / References: UniProt: Q7RTX0, UniProt: A0A1S4NYF2
#3: Polysaccharide 4-chloro-4-deoxy-alpha-D-galactopyranose-(1-2)-1,6-dichloro-1,6-dideoxy-beta-D-fructofuranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 397.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucralose
DescriptorTypeProgram
[][b-D-Fruf1chloro6chloro]{[(2+1)][a-D-Galp4chloro]{}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: heterodimer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84470 / Symmetry type: POINT
RefinementHighest resolution: 3.33 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048344
ELECTRON MICROSCOPYf_angle_d0.63311349
ELECTRON MICROSCOPYf_dihedral_angle_d4.9251111
ELECTRON MICROSCOPYf_chiral_restr0.0411257
ELECTRON MICROSCOPYf_plane_restr0.0061467

+
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