9KUV | pdb_00009kuv

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


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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

  • DOI: https://doi.org/10.1038/s41467-025-62870-z
  • Primary Citation of 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.


  • Organizational Affiliation
    • iHuman Institute, ShanghaiTech University, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-arrestin-scFv30621Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Apelin ReceptorB [auth R]506Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P35414 (Homo sapiens)
Explore P35414 
Go to UniProtKB:  P35414
PHAROS:  P35414
GTEx:  ENSG00000134817 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35414
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L6R
Query on A1L6R

Download Ideal Coordinates CCD File 
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
Query on CLR

Download Ideal Coordinates CCD File 
D [auth R]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
B [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
B [auth R]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

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