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- EMDB-72837: P2Y14R bound to MRS2905 (local refinement) -

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Basic information

Entry
Database: EMDB / ID: EMD-72837
TitleP2Y14R bound to MRS2905 (local refinement)
Map data
Sample
  • Complex: P2Y14R bound to MRS2905 (local refinement)
KeywordsGPCR / P2Y Receptor / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsFay JF
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Commun Biol / Year: 2025
Title: UDP-glucose and MRS2905 agonist-bound states of the purinergic P2Y receptor.
Authors: Jonathan F Fay / Joseph Kousouros / Zhan-Guo Gao / Matteo Pavan / Paola Oliva / Asmita Pramanik / Clayton Meyer / Siva Hariprasad Kurma / Wen Xu / Brian Krumm / Kenneth A Jacobson /
Abstract: P2Y receptors respond to uracil-diphosphate-hexose conjugates, yet how this receptor selectively recognizes both uracil-nucleotides and hexose moieties of diverse agonists remains unclear. Here we ...P2Y receptors respond to uracil-diphosphate-hexose conjugates, yet how this receptor selectively recognizes both uracil-nucleotides and hexose moieties of diverse agonists remains unclear. Here we report the active agonist-bound G protein-bound states of the P2Y G protein-coupled receptor (GPCR) bound to endogenous agonist uridine diphosphate glucose (UDP-glucose) and 2-thiouridine-5'-O-(α,β-methylene)diphosphate (MRS2905). The cryo-EM structures of the heterotrimeric complexes with 3.19 Å and 3.05 Å global resolution, respectively, with local refinements reaching 2.87 Å and 3.22 Å for the masked receptor region. Our structures reveal a pronounced extracellular facing electronegative vestibule connecting to a smaller nucleotide binding subpocket (~300Å volume) that is shielded by extracellular loop 2 (ECL2). A glucose-binding subpocket is spatially delimited by residue V93; mutation to Trp selectively blocks UDP-glucose while permitting MRS2905 and antagonist binding. These findings provide atomic insights into uracil recognition, reveal how the receptor accommodates diverse flexible UDP-sugars, and promise to enable rational drug discovery of therapeutic P2YR modulators.
History
DepositionSep 23, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72837.png

Downloads & links

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Map

FileDownload / File: emd_72837.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 288 pix.
= 264.355 Å		0.92 Å/pix.
x 288 pix.
= 264.355 Å		0.92 Å/pix.
x 288 pix.
= 264.355 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9179 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.0670336 - 2.835447
Average (Standard dev.)0.0005925715 (±0.014304089)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 264.3552 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72837_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72837_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : P2Y14R bound to MRS2905 (local refinement)

EntireName: P2Y14R bound to MRS2905 (local refinement)
Components
  • Complex: P2Y14R bound to MRS2905 (local refinement)

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Supramolecule #1: P2Y14R bound to MRS2905 (local refinement)

SupramoleculeName: P2Y14R bound to MRS2905 (local refinement) / type: complex / ID: 1 / Parent: 0
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-PROPANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 37.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.1 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 337217
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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