8XZG

Cryo-EM structure of the [Pyr1]-apelin-13-bound human APLNR-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-based design of non-hypertrophic apelin receptor modulator.

Wang, W.W.Ji, S.Y.Zhang, W.Zhang, J.Cai, C.Hu, R.Zang, S.K.Miao, L.Xu, H.Chen, L.N.Yang, Z.Guo, J.Qin, J.Shen, D.D.Liang, P.Zhang, Y.Zhang, Y.

(2024) Cell 187: 1460-1475.e20

  • DOI: https://doi.org/10.1016/j.cell.2024.02.004
  • Primary Citation of Related Structures:  
    8XZF, 8XZG, 8XZH, 8XZI, 8XZJ

  • PubMed Abstract: 

    Apelin is a key hormone in cardiovascular homeostasis that activates the apelin receptor (APLNR), which is regarded as a promising therapeutic target for cardiovascular disease. However, adverse effects through the β-arrestin pathway limit its pharmacological use. Here, we report cryoelectron microscopy (cryo-EM) structures of APLNR-G i1 complexes bound to three agonists with divergent signaling profiles. Combined with functional assays, we have identified "twin hotspots" in APLNR as key determinants for signaling bias, guiding the rational design of two exclusive G-protein-biased agonists WN353 and WN561. Cryo-EM structures of WN353- and WN561-stimulated APLNR-G protein complexes further confirm that the designed ligands adopt the desired poses. Pathophysiological experiments have provided evidence that WN561 demonstrates superior therapeutic effects against cardiac hypertrophy and reduced adverse effects compared with the established APLNR agonists. In summary, our designed APLNR modulator may facilitate the development of next-generation cardiovascular medications.


  • Organizational Affiliation

    Department of Pharmacology and Department of Pathology of Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; Center for Structural Pharmacology and Therapeutics Development, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
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Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1339Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Apelin-13D [auth L]13Homo sapiensMutation(s): 0 
Gene Names: APLNAPEL
Membrane Entity: Yes 
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Find proteins for Q9ULZ1 (Homo sapiens)
Explore Q9ULZ1 
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PHAROS:  Q9ULZ1
GTEx:  ENSG00000171388 
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UniProt GroupQ9ULZ1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Apelin receptorE [auth R]380Homo sapiensMutation(s): 0 
Gene Names: APLNRAGTRL1APJ
Membrane Entity: Yes 
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Find proteins for P35414 (Homo sapiens)
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PHAROS:  P35414
GTEx:  ENSG00000134817 
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
D [auth L]L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Structure summary