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 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.180 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A2GClick on this verticalbar to view detailsBest fitted NGAClick on this verticalbar to view details

This is version 1.2 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 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.180 (DCC) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A2GClick on this verticalbar to view detailsBest fitted NGAClick on this verticalbar to view details

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
  • Version 1.2: 2024-10-23
    Changes: Structure summary