8ZX5 | pdb_00008zx5

AM251-bound GPR55 in complex with G13

• PDB DOI: https://doi.org/10.2210/pdb8ZX5/pdb
• EM Map EMD-60538: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-06-13 Released: 2024-11-13 
• Deposition Author(s): He, Y., Xia, R.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insight into GPR55 ligand recognition and G-protein coupling.

Xia, R., Yuan, Q., Wang, N., Hou, L., Abe, J., Song, J., Ito, Y., Xu, H.E., He, Y.

(2025) Cell Res 35: 76-79

• PubMed: 39482404 
• DOI: https://doi.org/10.1038/s41422-024-01044-w
• Primary Citation of Related Structures:  
  8ZX4, 8ZX5

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Organizational Affiliation: 
• Laboratory of Receptor Structure and Signaling, HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
Osaka International Cancer Institute, Osaka, Osaka, Japan.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Laboratory of Receptor Structure and Signaling, HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China. [e-mail].
Frontiers Science Center for Matter Behave in Space Environment, Harbin Institute of Technology, Harbin, Heilongjiang, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 109.57 kDa 
• Atom Count: 6,106 
• Modeled Residue Count: 821 
• Deposited Residue Count: 965 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
engineered miniGalpha 13	A	230	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q14344 (Homo sapiens) Explore Q14344  Go to UniProtKB:  Q14344
PHAROS:  Q14344 GTEx:  ENSG00000120063

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	345	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor 55	D [auth R]	319	Homo sapiens	Mutation(s): 0  Gene Names: GPR55 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2T6 (Homo sapiens) Explore Q9Y2T6  Go to UniProtKB:  Q9Y2T6
PHAROS:  Q9Y2T6 GTEx:  ENSG00000135898

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D9D	E [auth R]	1-(2,4-dichlorophenyl)-5-(4-iodophenyl)-4-methyl-~{N}-piperidin-1-yl-pyrazole-3-carboxamide C22 H21 Cl2 I N4 O BUZAJRPLUGXRAB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): He, Y., Xia, R.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32070048

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection
• Version 1.2: 2025-01-22
  Changes: Data collection, Database references