9KFI | pdb_00009kfi

Cryo-EM structure of the human relaxin family peptide receptor 3 in complex with relaxin-3 and G protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular mechanism underlying non-discriminatory recognition of relaxin-3 by RXFP3 and RXFP4.

Chen, Y.Zhou, Q.Yan, S.Yan, J.Yang, D.Chen, J.Wang, M.W.

(2025) Commun Biol 8: 794-794

  • DOI: https://doi.org/10.1038/s42003-025-08220-7
  • Primary Citation of Related Structures:  
    9KFI, 9KFJ, 9KFK

  • PubMed Abstract: 

    The human relaxin family peptide receptors RXFP3 and RXFP4 play important physiological roles through interactions with endogenous hormones, relaxin-3 and insulin-like peptide 5 (INSL5). They are implicated in certain neurological and metabolic disorders. While INSL5 only activates RXFP4, relaxin-3 is recognized by both receptors. Here, we report the cryo-electron microscopy structures of RXFP3-G i complexes bound by relaxin-3 or a small-molecule dual agonist (compound 4), and relaxin-3 in complex with RXFP4-G i , with global resolutions of 2.91 Å, 2.95 Å, and 3.10 Å, respectively. It is found that relaxin-3 adopts a conserved binding conformation within the transmembrane domain (TMD) bundle of RXFP3 and RXFP4, where the C-terminal tip residues of its B chain, R26 and W27, make extensive contacts with conserved receptor residues, thereby activating RXFP3 and RXFP4. Compound 4 mimics these key interactions by binding to both receptors. In contrast, the C-terminal residues composition and TMD-binding angle of INSL5 in RXFP4 differ significantly from that of relaxin-3, ensuring its selectivity for RXFP4. These findings deepen our understanding about the structural basis of ligand recognition and selectivity in this G protein-coupled receptor subfamily.


  • Organizational Affiliation
    • Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Relaxin-3 receptor 1,LgBiTA [auth C]773Escherichia coliHomo sapienssynthetic construct
This entity is chimeric
Mutation(s): 3 
Gene Names: cybCRXFP3GPCR135RLN3R1SALPR
Membrane Entity: Yes 
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PHAROS:  Q9NSD7
GTEx:  ENSG00000182631 
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UniProt GroupQ9NSD7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2B [auth G]55Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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GTEx:  ENSG00000186469 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-2C [auth I]355Homo sapiensMutation(s): 4 
Gene Names: GNAI2GNAI2B
Membrane Entity: Yes 
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GTEx:  ENSG00000114353 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16D [auth S]248synthetic constructMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1E [auth T]338Homo sapiensMutation(s): 0 
Gene Names: GNB1
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GTEx:  ENSG00000078369 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Relaxin-3 B chainF [auth B]22Homo sapiensMutation(s): 0 
Gene Names: RLN3INSL7RXN3ZINS4UNQ6188/PRO20213
Membrane Entity: Yes 
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GTEx:  ENSG00000171136 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Relaxin-3 A chainG [auth A]24Homo sapiensMutation(s): 0 
Gene Names: RLN3INSL7RXN3ZINS4UNQ6188/PRO20213
Membrane Entity: Yes 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21704064
National Natural Science Foundation of China (NSFC)China82073904
National Natural Science Foundation of China (NSFC)China82121005

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release