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- EMDB-51342: Cryo-EM map of Thromboxane A2 receptor-Gq Protein Complex bound t... -

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Basic information

Entry
Database: EMDB / ID: EMD-51342
TitleCryo-EM map of Thromboxane A2 receptor-Gq Protein Complex bound to U46619 focused refined on the G proteins
Map dataSharpened cryo-EM map of Thromboxane A2 receptor-Gq Protein Complex bound to U46619 focused refined on the G proteins
Sample
  • Complex: Thromboxane A2 receptor-Gq Protein Complex
KeywordsSingle particle cryo-EM / GPCR / G-proteins / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsMatzov D / Krawinski P / Caffrey M / Shalev Benami M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)949364European Union
CitationJournal: Nat Commun / Year: 2026
Title: Structural and dynamic insights into agonist recognition and function of the thromboxane A receptor.
Authors: Pawel Krawinski / Donna Matzov / Aoife Ryder / Kanhaya Lal / Dmitry S Karlov / Georges Chalhoub / Eamon P Mulvaney / B Therese Kinsella / Peter J McCormick / Martin Caffrey / Irina G ...Authors: Pawel Krawinski / Donna Matzov / Aoife Ryder / Kanhaya Lal / Dmitry S Karlov / Georges Chalhoub / Eamon P Mulvaney / B Therese Kinsella / Peter J McCormick / Martin Caffrey / Irina G Tikhonova / Moran Shalev-Benami /
Abstract: The thromboxane A receptor (TP), expressed in platelets and smooth muscle, plays an important role in blood clotting and muscle contraction. The endogenous ligand of this G protein-coupled receptor ...The thromboxane A receptor (TP), expressed in platelets and smooth muscle, plays an important role in blood clotting and muscle contraction. The endogenous ligand of this G protein-coupled receptor (GPCR), thromboxane A (TXA), is a short-lived arachidonic acid metabolite with a half-life of ∼30 seconds, which makes investigating the TP structure and activation mechanism highly challenging. Here we determine the structures of the TP in complex with the synthetic agonists, U46619 and I-BOP, stable analogues of the natural ligand, in the presence of the signalling protein partner, G. The structures reveal a unique activation switch for the receptor that differs from typical class A GPCR family members. Complemented by functional studies, mutational analysis, docking, and molecular dynamics (MD) simulations, our investigation highlights the differences between agonist and antagonist binding and explores the ligand entry mechanism to the binding pocket from within the membrane via a molecular gate composed of two transmembrane helices. In addition, our study provides crucial information to aid in the rational design of compounds targeting the TP, and offers mechanistic insights into inherited disorders associated with mutations in the TP.
History
DepositionAug 14, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51342.png

Downloads & links

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Map

FileDownload / File: emd_51342.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryo-EM map of Thromboxane A2 receptor-Gq Protein Complex bound to U46619 focused refined on the G proteins
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 303.228 Å		0.84 Å/pix.
x 360 pix.
= 303.228 Å		0.84 Å/pix.
x 360 pix.
= 303.228 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8423 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-1.0133044 - 1.4124207
Average (Standard dev.)-0.00020161744 (±0.024929367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 303.228 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM map of Thromboxane A2 receptor-Gq Protein Complex...

Fileemd_51342_additional_1.map
AnnotationCryo-EM map of Thromboxane A2 receptor-Gq Protein Complex bound to U46619 focused refined on the G proteins
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of cryo-EM map of Thromboxane...

Fileemd_51342_half_map_1.map
AnnotationHalf map B of cryo-EM map of Thromboxane A2 receptor-Gq Protein Complex bound to U46619 focused refined on the G proteins
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 Thromboxane...

Fileemd_51342_half_map_2.map
AnnotationHalf map A of cryo-EM map of Thromboxane A2 receptor-Gq Protein Complex bound to U46619 focused refined on the G proteins
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Thromboxane A2 receptor-Gq Protein Complex

EntireName: Thromboxane A2 receptor-Gq Protein Complex
Components
  • Complex: Thromboxane A2 receptor-Gq Protein Complex

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Supramolecule #1: Thromboxane A2 receptor-Gq Protein Complex

SupramoleculeName: Thromboxane A2 receptor-Gq Protein Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.4 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 216383
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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