8H24

Leucine-rich alpha-2-glycoprotein 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


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Literature

Crystal structure of LRG1 and the functional significance of LRG1 glycan for LPHN2 activation.

Yang, J.Yin, G.N.Kim, D.K.Han, A.R.Lee, D.S.Min, K.W.Fu, Y.Yun, J.Suh, J.K.Ryu, J.K.Kim, H.M.

(2023) Exp Mol Med 55: 1013-1022

  • DOI: https://doi.org/10.1038/s12276-023-00992-4
  • Primary Citation of Related Structures:  
    8H24

  • PubMed Abstract: 

    The serum glycoprotein leucine-rich ɑ-2-glycoprotein 1 (LRG1), primarily produced by hepatocytes and neutrophils, is a multifunctional protein that modulates various signaling cascades, mainly TGFβ signaling. Serum LRG1 and neutrophil-derived LRG1 have different molecular weights due to differences in glycosylation, but the impact of the differential glycan composition in LRG1 on its cellular function is largely unknown. We previously reported that LRG1 can promote both angiogenic and neurotrophic processes under hyperglycemic conditions by interacting with LPHN2. Here, we determined the crystal structure of LRG1, identifying the horseshoe-like solenoid structure of LRG1 and its four N-glycosylation sites. In addition, our biochemical and cell-biological analyses found that the deglycosylation of LRG1, particularly the removal of glycans on N325, is critical for the high-affinity binding of LRG1 to LPHN2 and thus promotes LRG1/LPHN2-mediated angiogenic and neurotrophic processes in mouse tissue explants, even under normal glucose conditions. Moreover, the intracavernous administration of deglycosylated LRG1 in a diabetic mouse model ameliorated vascular and neurological abnormalities and restored erectile function. Collectively, these data indicate a novel role of LRG1 glycans as molecular switches that can tune the range of LRG1's cellular functions, particularly the LRG1/LPHN2 signaling axis.


  • Organizational Affiliation

    Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich alpha-2-glycoprotein347Homo sapiensMutation(s): 0 
Gene Names: LRG1LRG
UniProt & NIH Common Fund Data Resources
Find proteins for P02750 (Homo sapiens)
Explore P02750 
Go to UniProtKB:  P02750
PHAROS:  P02750
GTEx:  ENSG00000171236 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02750
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.018α = 90
b = 143.018β = 90
c = 113.728γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentKorea, Republic OfIBS-R030-C1

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release