7YQE

Structure of human SRC regulatory domains in complex with the C-terminal PRRP motifs of GPR54.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.270 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Kisspeptin-10 binding to Gpr54 in osteoclasts prevents bone loss by activating Dusp18-mediated dephosphorylation of Src.

Li, Z.Yang, X.Fu, R.Wu, Z.Xu, S.Jiao, J.Qian, M.Zhang, L.Wu, C.Xie, T.Yao, J.Wu, Z.Li, W.Ma, G.You, Y.Chen, Y.Zhang, H.K.Cheng, Y.Tang, X.Wu, P.Lian, G.Wei, H.Zhao, J.Xu, J.Ai, L.Siwko, S.Wang, Y.Ding, J.Song, G.Luo, J.Liu, M.Xiao, J.

(2024) Nat Commun 15: 1300-1300

  • DOI: https://doi.org/10.1038/s41467-024-44852-9
  • Primary Citation of Related Structures:  
    7YQE

  • PubMed Abstract: 

    Osteoclasts are over-activated as we age, which results in bone loss. Src deficiency in mice leads to severe osteopetrosis due to a functional defect in osteoclasts, indicating that Src function is essential in osteoclasts. G-protein-coupled receptors (GPCRs) are the targets for ∼35% of approved drugs but it is still unclear how GPCRs regulate Src kinase activity. Here, we reveal that GPR54 activation by its natural ligand Kisspeptin-10 (Kp-10) causes Dusp18 to dephosphorylate Src at Tyr 416. Mechanistically, Gpr54 recruits both active Src and the Dusp18 phosphatase at its proline/arginine-rich motif in its C terminus. We show that Kp-10 binding to Gpr54 leads to the up-regulation of Dusp18. Kiss1, Gpr54 and Dusp18 knockout mice all exhibit osteoclast hyperactivation and bone loss, and Kp-10 abrogated bone loss by suppressing osteoclast activity in vivo. Therefore, Kp-10/Gpr54 is a promising therapeutic target to abrogate bone resorption by Dusp18-mediated Src dephosphorylation.


  • Organizational Affiliation

    Institute of Orthopedic Biomedical and Device Innovation, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China. zxli@usst.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src,KiSS-1 receptor
A, B
188Homo sapiensMutation(s): 2 
Gene Names: SRCSRC1KISS1RAXOR12GPR54
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q969F8 (Homo sapiens)
Explore Q969F8 
Go to UniProtKB:  Q969F8
PHAROS:  Q969F8
GTEx:  ENSG00000116014 
Find proteins for P12931 (Homo sapiens)
Explore P12931 
Go to UniProtKB:  P12931
PHAROS:  P12931
GTEx:  ENSG00000197122 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ969F8P12931
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.270 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.245α = 90
b = 95.245β = 90
c = 122.82γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

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: 2023-08-16
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Database references