9KUV | pdb_00009kuv

Mechanistic insights into the versatile stoichiometry and biased signaling of the apelin receptor-arrestin complex

• PDB DOI: https://doi.org/10.2210/pdb9KUV/pdb
• EM Map EMD-62581: EMDB EMDataResource

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


• Deposited: 2024-12-04 Released: 2025-09-17 
• Deposition Author(s): Yue, Y., Wu, L.J., Xu, F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanistic insights into the versatile stoichiometry and biased signaling of the apelin receptor-arrestin complex.

Yue, Y., Xu, C., Wu, L., Na, M., Xu, K., Chen, X., Song, Y., Weng, S., Xu, L., Li, F., Lin, X., Wang, A., Liu, J., Xu, F.

(2025) Nat Commun 16: 7403-7403

• PubMed: 40790299 
• DOI: https://doi.org/10.1038/s41467-025-62870-z
• Primary Citation Related Structures: 
  9KUV, 9KUW, 9KUX


• PubMed Abstract: 
  

  The apelin receptor (APJR) plays a pivotal role in regulating cardiovascular and metabolic health ^1,2 . Understanding the mechanisms of biased agonism at APJR is crucial for drug discovery, as stimulation of the β-arrestin pathway may lead to some adverse effects ³ . Structural analyses of APJR-Gi complexes have clarified the structural basis of receptor dimerization and activation ^4,5 , yet the absence of structural data on APJR-arrestin complexes has impeded a comprehensive understanding of APJR stoichiometry in the dual signaling pathways and biased agonism. Here, we present APJR-β-arrestin1 structures bound to a clinical drug analog, revealing 2:2 and 2:1 stoichiometries associated with differential β-arrestin recruitment. Through comparison of the two transducer-coupled APJR structures bound to the same ligand, we identify key residues and motifs crucial for directing biased signaling. These findings highlight APJR's versatile stoichiometry in coupling with β-arrestin and Gi proteins, establishing a framework for understanding biased agonism and guiding the development of therapeutics.

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Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai, China.
Key Laboratory of Molecular Biophysics of MOE, International Research Center for Sensory Biology and Technology of MOST, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
JiKang Therapeutics, Shanghai, China.
Key Laboratory of Molecular Biophysics of MOE, International Research Center for Sensory Biology and Technology of MOST, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China. [e-mail].
iHuman Institute, ShanghaiTech University, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
JiKang Therapeutics, Shanghai, China. [e-mail].
Shanghai Clinical Research and Trial Center, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 126.87 kDa 
• Atom Count: 7,102 
• Modeled Residue Count: 894 
• Deposited Residue Count: 1,127 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-arrestin-scFv30	A	621	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Apelin Receptor	B [auth R]	506	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P35414 (Homo sapiens) Explore P35414  Go to UniProtKB:  P35414
PHAROS:  P35414 GTEx:  ENSG00000134817

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L6R	C [auth R]	(1~{S},2~{S})-~{N}-[4-(2,6-dimethoxyphenyl)-5-(6-methylpyridin-2-yl)-1,2,4-triazol-3-yl]-1-(5-methylpyrimidin-2-yl)-1-oxidanyl-propane-2-sulfonamide C24 H27 N7 O5 S HNGYVRSMVVCWGF-HRAATJIYSA-N
CLR	D [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Yue, Y., Wu, L.J., Xu, F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release