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 9KPE | pdb_00009kpe

Cryo-EM structure of GPCR16-GiH5 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9KPE

This is version 1.1 of the entry. See complete history. 

Literature

Structural basis of beta-glucopyranoside salicin recognition by a human bitter taste GPCR.

Wang, X., Zhou, C., Ao, W., Wu, L., Wu, Y., Xu, W., Liu, S., Tan, Q., Wang, L., Zhao, F., Liu, J., Pei, Y., Zhao, S., Hua, T.

(2025) Cell Rep 44: 115604-115604

  • DOI: https://doi.org/10.1016/j.celrep.2025.115604
  • Primary Citation Related Structures: 
    9K6L, 9KPD, 9KPE, 9KPF

  • PubMed Abstract: 

    The human perception of bitterness is mediated by type 2 taste receptors (TAS2Rs), which recognize a broad array of bitter substances with distinct chemical properties. TAS2R16 exhibits a pronounced selectivity for β-glucoside-moiety-containing compounds, such as salicin from willow bark. However, the molecular mechanism of moiety-specific recognition and receptor activation in TAS2R16 remains unclear. Here, we present cryoelectron microscopy structures of the salicin-activated human TAS2R16 complexed with gustducin and G i1 and G i2 proteins. The binding mode of salicin with TAS2R16 and the specific interactions of the β-D-glucopyranoside moiety are detailed. Together with molecular docking and mutagenesis data, this study uncovers the structural underpinnings of TAS2R16's group-specific recognition, receptor activation, and subsequent gustducin and G i protein coupling. These findings advance our understanding of human bitter taste receptors and provide a foundation for structural modifications of bitter glycosides, opening potential therapeutic applications.


  • Organizational Affiliation: 
    • iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.

Macromolecule Content 

  • Total Structure Weight: 232.59 kDa 
  • Atom Count: 8,916 
  • Modeled Residue Count: 1,127 
  • Deposited Residue Count: 2,082 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1368Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
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UniProt GroupP63096
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1366Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
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UniProt GroupP59768
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Fusion protein 1,exo-alpha-sialidase,Taste receptor type 2 member 16,Fusion protein 2D [auth R]1,011Homo sapiens, Streptococcus pneumoniaeMutation(s): 0 
EC: 3.2.1.18
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYV7 (Homo sapiens)
Explore Q9NYV7 
Go to UniProtKB:  Q9NYV7
PHAROS:  Q9NYV7
GTEx:  ENSG00000128519 
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UniProt GroupQ9NYV7
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16E [auth S]266Homo sapiensMutation(s): 0 
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SA0
(Subject of Investigation/LOI)

Query on SA0



Download:Ideal Coordinates CCD File
F [auth R]2-(hydroxymethyl)phenyl beta-D-glucopyranoside
C13 H18 O7
NGFMICBWJRZIBI-UJPOAAIJSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB37030104

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-10-15
    Changes: Data collection, Database references