8R8C

Structure of the N-terminal domain of CMA from Cucumis melo in complex with N-acetylgalactosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin.

Lundstrom, J.Gillon, E.Chazalet, V.Kerekes, N.Di Maio, A.Feizi, T.Liu, Y.Varrot, A.Bojar, D.

(2024) Beilstein J Org Chem 20: 306-320

  • DOI: https://doi.org/10.3762/bjoc.20.31
  • Primary Citation of Related Structures:  
    8R8A, 8R8C

  • PubMed Abstract: 

    Plant lectins have garnered attention for their roles as laboratory probes and potential therapeutics. Here, we report the discovery and characterization of Cucumis melo agglutinin (CMA1), a new R-type lectin from melon. Our findings reveal CMA1's unique glycan-binding profile, mechanistically explained by its 3D structure, augmenting our understanding of R-type lectins. We expressed CMA1 recombinantly and assessed its binding specificity using multiple glycan arrays, covering 1,046 unique sequences. This resulted in a complex binding profile, strongly preferring C2-substituted, beta-linked galactose (both GalNAc and Fuca1-2Gal), which we contrasted with the established R-type lectin Ricinus communis agglutinin 1 (RCA1). We also report binding of specific glycosaminoglycan subtypes and a general enhancement of binding by sulfation. Further validation using agglutination, thermal shift assays, and surface plasmon resonance confirmed and quantified this binding specificity in solution. Finally, we solved the high-resolution structure of the CMA1 N-terminal domain using X-ray crystallography, supporting our functional findings at the molecular level. Our study provides a comprehensive understanding of CMA1, laying the groundwork for further exploration of its biological and therapeutic potential.


  • Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 7B, 413 90 Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nigrin b-like130Cucumis meloMutation(s): 0 
Gene Names: LOC107992255107992255
UniProt
Find proteins for A0A1S4E5V9 (Cucumis melo)
Explore A0A1S4E5V9 
Go to UniProtKB:  A0A1S4E5V9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S4E5V9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.163 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.613α = 90
b = 36.86β = 99.166
c = 94.813γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-12-27 
  • Deposition Author(s): Varrot, A.

Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references