9IJR | pdb_00009ijr

Cryo-EM structure of the orphan GPR52 beta-arrestin 1 complex bound to ligand c17

• PDB DOI: https://doi.org/10.2210/pdb9IJR/pdb
• EM Map EMD-60642: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-06-25 Released: 2025-09-03 
• Deposition Author(s): Lin, X., Xu, F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.86 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Constitutive arrestin recruitment by orphan GPR52 via an atypical binding mode.

Lin, X., Wei, X., Pu, N., Wang, L., Zhang, Z., Li, C., Yue, Y., Liu, J., Tan, Q., Sun, Q., Xu, F.

(2025) Cell Res 35: 913-916

• PubMed: 40813798 
• DOI: https://doi.org/10.1038/s41422-025-01165-w
• Primary Citation Related Structures: 
  9IJR, 9IJS

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Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
iHuman Institute, ShanghaiTech University, Shanghai, China.
iHuman Institute, ShanghaiTech University, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].

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: 115.17 kDa 
• Atom Count: 6,136 
• Modeled Residue Count: 873 
• Deposited Residue Count: 1,028 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor 52	A	369	Homo sapiens	Mutation(s): 0  Gene Names: GPR52 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2T5 (Homo sapiens) Explore Q9Y2T5  Go to UniProtKB:  Q9Y2T5
PHAROS:  Q9Y2T5 GTEx:  ENSG00000203737

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-arrestin-1	B [auth C]	393	Homo sapiens	Mutation(s): 0  Gene Names: ARRB1, ARR1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P49407 (Homo sapiens) Explore P49407  Go to UniProtKB:  P49407
PHAROS:  P49407 GTEx:  ENSG00000137486

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv30 antibody	C [auth H]	266	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EN6	D [auth A]	N-(2-hydroxyethyl)-5-(hydroxymethyl)-3-methyl-1-[2-[[3-(trifluoromethyl)phenyl]methyl]-1-benzothiophen-7-yl]pyrazole-4-carboxamide C24 H22 F3 N3 O3 S VJMRKWPMFQGIPI-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.86 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Lin, X., Xu, F.

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

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release
  
• Version 1.1: 2025-11-19
  Changes: Data collection, Database references