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- EMDB-69813: P2Y14R-Gi complex bound to UDP (consensus) -

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Basic information

Entry
Database: EMDB / ID: EMD-69813
TitleP2Y14R-Gi complex bound to UDP (consensus)
Map data
Sample
  • Complex: P2Y13R-Gq complex bound to ADP
KeywordsGPCR / Nucleotide / G protein / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsOshima HS / Akasaka H / Sano FK / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H05037 Japan
CitationJournal: Biochem Biophys Res Commun / Year: 2026
Title: Structural insights into the ligand and G protein recognition by P2YR.
Authors: Hidetaka S Oshima / Hiroaki Akasaka / Fumiya K Sano / Osamu Nureki /
Abstract: P2Y purinergic receptors are GPCRs that recognize extracellular nucleotides to mediate diverse physiological processes. Among 12-like subfamily members, P2YR has well-documented roles in ...P2Y purinergic receptors are GPCRs that recognize extracellular nucleotides to mediate diverse physiological processes. Among 12-like subfamily members, P2YR has well-documented roles in neuroprotection and cholesterol metabolism. Notably, P2YR displays robust activity toward the G pathway in addition to its canonical G coupling, yet the structural basis for its ligand recognition and G protein selectivity has remained unclear. Here, we present the cryo-EM structure of the P2YR-G complex bound to ADP at a resolution of 2.83 Å. The structure reveals the distinctive ligand recognition mechanism of P2YR, in which an N-terminal arginine caps the orthosteric binding pocket. Furthermore, we also elucidated the structure of P2YR, which shows the lowest G activation ability among the 12-like P2Y receptors, in complex with UDP and G at a resolution of 2.93 Å. Structural comparison with the 12-like P2Y receptors implicates ICL2-mediated contacts with the Gα hydrophobic cavity as a key structural determinant of G selectivity. Together, these findings provide mechanistic insights into nucleotide signaling and a structural foundation for advancing structure-based approaches to targeting the 12-like P2Y receptors.
History
DepositionMar 20, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_69813.png

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Map

FileDownload / File: emd_69813.map.gz / Format: CCP4 / Size: 52.7 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.)
1.11 Å/pix.
x 240 pix.
= 265.608 Å		1.11 Å/pix.
x 240 pix.
= 265.608 Å		1.11 Å/pix.
x 240 pix.
= 265.608 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.494
Minimum - Maximum-1.5606238 - 3.17253
Average (Standard dev.)-0.0046334118 (±0.07464711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 265.60797 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_69813_half_map_1.map
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AxesZYX

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Half map: #2

Fileemd_69813_half_map_2.map
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Sample components

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Entire : P2Y13R-Gq complex bound to ADP

EntireName: P2Y13R-Gq complex bound to ADP
Components
  • Complex: P2Y13R-Gq complex bound to ADP

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Supramolecule #1: P2Y13R-Gq complex bound to ADP

SupramoleculeName: P2Y13R-Gq complex bound to ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2, #4-#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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 170129
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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