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- EMDB-71038: Consensus map for Gi-coupled TAS2R43 with aristolochic acid I -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-71038
TitleConsensus map for Gi-coupled TAS2R43 with aristolochic acid I
Map data
Sample
  • Complex: GPCR complex 1
KeywordsGPCR / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKim Y / Gumpper RH / Roth BL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)U24 DK116195 United States
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Structural insights into coffee bitter taste perception by TAS2R43 receptor.
Authors: Yoojoong Kim / Ryan H Gumpper / Yuxuan Zhuang / Ron O Dror / Bryan L Roth /
Abstract: Bitter taste functions as a means of both protection against potentially toxic compounds and savoring bitter tasting foods and beverages. Among the 26 bitter taste receptors, taste receptor type 2 ...Bitter taste functions as a means of both protection against potentially toxic compounds and savoring bitter tasting foods and beverages. Among the 26 bitter taste receptors, taste receptor type 2 member 43 (TAS2R43) has been identified as key for recognizing the bitter taste of coffee. TAS2R43 has also been implicated in many other physiological processes, including the regulation of glucagon-like peptide 1 release from the intestine, bronchodilation, innate immunity and metabolism. Here we report cryo-electron microscopy structures of human TAS2R43 coupled with inhibitory G protein or gustducin (G) stabilized by the potent nephrotoxin and carcinogen aristolochic acid I. Both structures revealed that aristolochic acid I binds in a presumed orthosteric pocket shared with other bitter taste receptor. Further structural, functional and computational studies revealed potential modes for coffee's constituents including caffeine and cafestol, which are bitter tastants from coffee. Lastly, long-timescale molecular dynamics simulations identified potential cryptic allosteric pockets in TAS2R43. These structures could accelerate the search for specific bitter taste ligands that ultimately may be therapeutically useful.
History
DepositionJun 4, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71038.png

Downloads & links

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Map

FileDownload / File: emd_71038.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 288 pix.
= 252.288 Å		0.88 Å/pix.
x 288 pix.
= 252.288 Å		0.88 Å/pix.
x 288 pix.
= 252.288 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.876 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.3785393 - 5.4715796
Average (Standard dev.)-0.0022446485 (±0.09606629)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 252.288 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71038_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71038_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GPCR complex 1

EntireName: GPCR complex 1
Components
  • Complex: GPCR complex 1

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Supramolecule #1: GPCR complex 1

SupramoleculeName: GPCR complex 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration7 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8vy7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 583017
Initial angle assignmentType: OTHER / Details: cryoSPARC ab-initio
Final angle assignmentType: ANGULAR RECONSTITUTION

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