8YMD | pdb_00008ymd

Galectin-3 with lychnose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 
    0.159 (Depositor), 0.162 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.143 (DCC) 
  • R-Value Observed: 
    0.141 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Oligosaccharides from Stellaria dichotoma L. var. lanceolate bind to galectin-3 and ameliorate effects of colitis.

Zhao, Z.Wu, J.Xu, X.He, Z.Wang, X.Su, J.Mayo, K.H.Sun, L.Cui, L.Zhou, Y.

(2024) Carbohydr Polym 345: 122551-122551

  • DOI: https://doi.org/10.1016/j.carbpol.2024.122551
  • Primary Citation of Related Structures:  
    8YMD

  • PubMed Abstract: 

    Even though Stellaria dichotoma L. var. lanceolate (S. dichotoma) is a well-known medicinal plant in the family Caryophyllaceae, its oligosaccharides remain unexplored in terms of their potential as bioactive agents. Here, we isolated a mixture of oligosaccharides from S. dichotoma (Yield: 12 % w/w), that are primarily non-classical raffinose family oligosaccharides (RFOs). Nine major oligosaccharides were purified and identified from the mixture, including sucrose, raffinose, 1-planteose, lychnose, stellariose, along with four new non-classical RFOs. Two of the four new oligosaccharides are linear hexose pentamers with α-galactosyl extensions on their lychnose moieties, and the other two are branched hexose hexamers with α-galactosyl extensions on their stellariose groups. Their interactions with galectin-3 (Gal-3) revealed significant binding, with the terminal galactose providing enhanced affinity for the lectin. Notably, Gal-3 residues Arg144, His158, Asn160, Arg162, Asn174, Trp181, Glu184 and Arg186 coordinate with the lychnose. In vivo studies using the dextran sulfate sodium (DSS) mouse model for colitis demonstrated the ability of these carbohydrates in mitigating ulcerative colitis (UC). Overall, our study has provided structural information and potential applications of S. dichotoma oligosaccharides, also offers new approaches for the development of medicinal oligosaccharides.


  • Organizational Affiliation

    Engineering Research Center of Glycoconjugates, Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-3140Homo sapiensMutation(s): 0 
Gene Names: LGALS3MAC2
UniProt & NIH Common Fund Data Resources
Find proteins for P17931 (Homo sapiens)
Explore P17931 
Go to UniProtKB:  P17931
PHAROS:  P17931
GTEx:  ENSG00000131981 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17931
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-[alpha-D-galactopyranose-(1-1)]beta-D-fructofuranose
B
4N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free:  0.159 (Depositor), 0.162 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.143 (DCC) 
  • R-Value Observed: 0.141 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.886α = 90
b = 57.383β = 90
c = 61.716γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-02-12 
  • Deposition Author(s): Su, J.Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171255

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release