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 9YDU | pdb_00009ydu

UDPG bound P2Y14 Receptor in complex with Gi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9YDU

This is version 1.2 of the entry. See complete history. 

Literature

UDP-glucose and MRS2905 agonist-bound states of the purinergic P2Y 14 receptor.

Fay, J.F., Kousouros, J., Gao, Z.G., Pavan, M., Oliva, P., Pramanik, A., Meyer, C., Kurma, S.H., Xu, W., Krumm, B., Jacobson, K.A.

(2025) Commun Biol 8: 1816-1816

  • DOI: https://doi.org/10.1038/s42003-025-09174-6
  • Primary Citation Related Structures: 
    9YDU, 9YDV

  • PubMed Abstract: 

    P2Y 14 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 14 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 3 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 P2Y 14 R modulators.


  • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, Baltimore, MD, USA. jfay@som.umaryland.edu.

Macromolecule Content 

  • Total Structure Weight: 151.88 kDa 
  • Atom Count: 8,859 
  • Modeled Residue Count: 1,127 
  • Deposited Residue Count: 1,354 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1A [auth B]354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B [auth C]340Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth D]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16D [auth E]251Mus musculusMutation(s): 0 
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
P2Y purinoceptor 14E [auth A]338Homo sapiensMutation(s): 0 
Gene Names: P2RY14, GPR105, KIAA0001
UniProt & NIH Common Fund Data Resources
Find proteins for Q15391 (Homo sapiens)
Explore Q15391 
Go to UniProtKB:  Q15391
PHAROS:  Q15391
GTEx:  ENSG00000174944 
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UniProt GroupQ15391
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UPG
(Subject of Investigation/LOI)

Query on UPG



Download:Ideal Coordinates CCD File
F [auth A]URIDINE-5'-DIPHOSPHATE-GLUCOSE
C15 H24 N2 O17 P2
HSCJRCZFDFQWRP-JZMIEXBBSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-11-19 
  • Deposition Author(s): Fay, J.F.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references
  • Version 1.2: 2026-01-07
    Changes: Data collection, Database references