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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9ECJ

This is version 1.1 of the entry. See complete history.

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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86VZ1
Sequence Annotations Expand
Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14344
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BIG (Subject of Investigation/LOI) Query on A1BIG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	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		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Billesboelle, C.B.

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

Revision History (Full details and data files)

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