9ECJ | pdb_00009ecj

Human P2RY8 bound to S-geranylgeranyl-L-glutathione in complex with miniG13

• PDB DOI: https://doi.org/10.2210/pdb9ECJ/pdb
• EM Map EMD-47912: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2024-11-14 Released: 2025-11-05 
• Deposition Author(s): Billesboelle, C.B., Manglik, A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Human P2RY8 bound to S-geranylgeranyl-L-glutathione in complex with miniG13

LaFlam, T.N., Billesboelle, C.B., Dihn, T., Wolfreys, F.D., Lu, E., Matteson, T., Jinping, A., Xu, Y., Singhal, A., Brandes, N., Ntranos, V., Manglik, A., Cyster, J.G., Ye, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 112.34 kDa 
• Atom Count: 6,323 
• Modeled Residue Count: 790 
• Deposited Residue Count: 994 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2Y purinoceptor 8	A [auth B]	384	Homo sapiens	Mutation(s): 0  Gene Names: P2RY8
UniProt & NIH Common Fund Data Resources
Find proteins for Q86VZ1 (Homo sapiens) Explore Q86VZ1  Go to UniProtKB:  Q86VZ1
PHAROS:  Q86VZ1 GTEx:  ENSG00000182162

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein subunit alpha-13	B [auth C]	240	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q14344 (Homo sapiens) Explore Q14344  Go to UniProtKB:  Q14344
PHAROS:  Q14344 GTEx:  ENSG00000120063

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C [auth D]	370	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BIG (Subject of Investigation/LOI)	D [auth B]	L-gamma-glutamyl-S-[(2Z,6E)-3,7,15-trimethyl-11-methylidenehexadeca-2,6,14-trien-1-yl]-L-cysteinylglycine C30 H49 N3 O6 S BAJIBEVLRWVBAZ-WKALPULASA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Billesboelle, C.B., Manglik, A.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release
  
• Version 1.1: 2025-11-12
  Changes: Data collection