Crystal Structure of Caenorhabditis elegans galectin LEC-6

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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Structural basis of preferential binding of fucose-containing saccharide by the Caenorhabditis elegans galectin LEC-6

Makyio, H.Takeuchi, T.Tamura, M.Nishiyama, K.Takahashi, H.Natsugari, H.Arata, Y.Kasai, K.Yamada, Y.Wakatsuki, S.Kato, R.

(2013) Glycobiology 23: 797-805

  • DOI: https://doi.org/10.1093/glycob/cwt017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Galectins are a group of lectins that can bind carbohydrate chains containing β-galactoside units. LEC-6, a member of galectins of Caenorhabditis elegans, binds fucose-containing saccharides. We solved the crystal structure of LEC-6 in complex with galactose-β1,4-fucose (Galβ1-4Fuc) at 1.5 Å resolution. The overall structure of the protein and the identities of the amino-acid residues binding to the disaccharide are similar to those of other galectins. However, further structural analysis and multiple sequence alignment between LEC-6 and other galectins indicate that a glutamic acid residue (Glu67) is important for the preferential binding between LEC-6 and the fucose moiety of the Galβ1-4Fuc unit. Frontal affinity chromatography analysis indicated that the affinities of E67D and E67A mutants for Galβ1-4Fuc are lower than that of wild-type LEC-6. Furthermore, the affinities of Glu67 mutants for an endogenous oligosaccharide, which contains a Galβ1-4Fuc unit, are drastically reduced relative to that of the wild-type protein. We conclude that the Glu67 in the oligosaccharide-binding site assists the recognition of the fucose moiety by LEC-6.

  • Organizational Affiliation

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization KEK, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LEC-6
A, B
160Caenorhabditis elegansMutation(s): 0 
Gene Names: lec-6
Find proteins for Q9N384 (Caenorhabditis elegans)
Explore Q9N384 
Go to UniProtKB:  Q9N384
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9N384
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G61266PA
GlyCosmos:  G61266PA
GlyGen:  G61266PA
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.323α = 90
b = 69.323β = 90
c = 120.131γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-03-20
    Changes: Data collection, Database references, Structure summary