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- EMDB-19744: TAS2R14 receptor bound to flufenamic acid and gustducin -

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Basic information

Entry
Database: EMDB / ID: EMD-19744
TitleTAS2R14 receptor bound to flufenamic acid and gustducin
Map dataCryo-EM sharpened map of TAS2R14 in complex with G-proteins after local refinement of the receptor
Sample
  • Complex: Human Taste receptor type 2 member 14 in complex with G-proteins
KeywordsSingle particle cryo-EM / GPCR / G-protein / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsMatzov D / Peri L / Niv M / Shalev Benami M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)949364European Union
CitationJournal: Nat Commun / Year: 2024
Title: A bitter anti-inflammatory drug binds at two distinct sites of a human bitter taste GPCR.
Authors: Lior Peri / Donna Matzov / Dominic R Huxley / Alon Rainish / Fabrizio Fierro / Liel Sapir / Tara Pfeiffer / Lukas Waterloo / Harald Hübner / Yoav Peleg / Peter Gmeiner / Peter J McCormick / ...Authors: Lior Peri / Donna Matzov / Dominic R Huxley / Alon Rainish / Fabrizio Fierro / Liel Sapir / Tara Pfeiffer / Lukas Waterloo / Harald Hübner / Yoav Peleg / Peter Gmeiner / Peter J McCormick / Dorothee Weikert / Masha Y Niv / Moran Shalev-Benami /
Abstract: Bitter taste receptors (TAS2Rs), a subfamily of G-protein coupled receptors (GPCRs) expressed orally and extraorally, elicit signaling in response to a large set of tastants. Among 25 functional ...Bitter taste receptors (TAS2Rs), a subfamily of G-protein coupled receptors (GPCRs) expressed orally and extraorally, elicit signaling in response to a large set of tastants. Among 25 functional TAS2Rs encoded in the human genome, TAS2R14 is the most promiscuous, and responds to hundreds of chemically diverse ligands. Here we present the cryo-electron microscopy (cryo-EM) structure of the human TAS2R14 in complex with its signaling partner gustducin, and bound to flufenamic acid (FFA), a clinically approved nonsteroidal anti-inflammatory drug. The structure reveals an unusual binding mode, where two copies of FFA are bound at distinct pockets: one at the canonical receptor site within the trans-membrane bundle, and the other in the intracellular facet, bridging the receptor with gustducin. Together with a pocket-specific BRET-based ligand binding assay, these results illuminate bitter taste signaling and provide tools for a site-targeted compound design.
History
DepositionFeb 25, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJan 8, 2025-
Current statusJan 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19744.png

Downloads & links

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Map

FileDownload / File: emd_19744.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM sharpened map of TAS2R14 in complex with G-proteins after local refinement of the receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.307
Minimum - Maximum-1.4284246 - 1.819385
Average (Standard dev.)-0.00025488404 (±0.021736778)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM map of TAS2R14 in complex with G-proteins...

Fileemd_19744_additional_1.map
AnnotationCryo-EM map of TAS2R14 in complex with G-proteins after local refinement of the receptor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of cryo-EM map of TAS2R14...

Fileemd_19744_half_map_1.map
AnnotationHalf map A of cryo-EM map of TAS2R14 in complex with G-proteins after local refinement of the receptor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of cryo-EM map of TAS2R14...

Fileemd_19744_half_map_2.map
AnnotationHalf map A of cryo-EM map of TAS2R14 in complex with G-proteins after local refinement of the receptor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Taste receptor type 2 member 14 in complex with G-proteins

EntireName: Human Taste receptor type 2 member 14 in complex with G-proteins
Components
  • Complex: Human Taste receptor type 2 member 14 in complex with G-proteins

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Supramolecule #1: Human Taste receptor type 2 member 14 in complex with G-proteins

SupramoleculeName: Human Taste receptor type 2 member 14 in complex with G-proteins
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.3 kDa/nm

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 20.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127503
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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