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 2WKK | pdb_00002wkk

Identification of the glycan target of the nematotoxic fungal galectin CGL2 in Caenorhabditis elegans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.186 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.147 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2WKK

This is version 2.1 of the entry. See complete history. 

Literature

Caenorhabditis Elegans N-Glycan Core Beta-Galactoside Confers Sensitivity Towards Nematotoxic Fungal Galectin Cgl2.

Butschi, A., Titz, A., Walti, M.A., Olieric, V., Paschinger, K., Nobauer, K., Guo, X., Seeberger, P.H., Wilson, I.B.H., Aebi, M., Hengartner, M.O., Kunzler, M.

(2010) PLoS Pathog 6: E717

  • DOI: https://doi.org/10.1371/journal.ppat.1000717
  • Primary Citation Related Structures: 
    2WKK

  • PubMed Abstract: 

    The physiological role of fungal galectins has remained elusive. Here, we show that feeding of a mushroom galectin, Coprinopsis cinerea CGL2, to Caenorhabditis elegans inhibited development and reproduction and ultimately resulted in killing of this nematode. The lack of toxicity of a carbohydrate-binding defective CGL2 variant and the resistance of a C. elegans mutant defective in GDP-fucose biosynthesis suggested that CGL2-mediated nematotoxicity depends on the interaction between the galectin and a fucose-containing glycoconjugate. A screen for CGL2-resistant worm mutants identified this glycoconjugate as a Galbeta1,4Fucalpha1,6 modification of C. elegans N-glycan cores. Analysis of N-glycan structures in wild type and CGL2-resistant nematodes confirmed this finding and allowed the identification of a novel putative glycosyltransferase required for the biosynthesis of this glycoepitope. The X-ray crystal structure of a complex between CGL2 and the Galbeta1,4Fucalpha1,6GlcNAc trisaccharide at 1.5 A resolution revealed the biophysical basis for this interaction. Our results suggest that fungal galectins play a role in the defense of fungi against predators by binding to specific glycoconjugates of these organisms.


  • Organizational Affiliation: 
    • Institute of Molecular Biology, University of Zürich, Zürich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 68.9 kDa 
  • Atom Count: 5,740 
  • Modeled Residue Count: 600 
  • Deposited Residue Count: 600 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GALECTIN-2
A, B, C, D
150Coprinopsis cinereaMutation(s): 0 
UniProt
Find proteins for Q9P4R8 (Coprinopsis cinerea)
Explore Q9P4R8 
Go to UniProtKB:  Q9P4R8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P4R8
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-alpha-L-fucopyranose
E
2N/A
Glycosylation Resources
GlyTouCan: G61266PA
GlyCosmos: G61266PA
GlyGen: G61266PA
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, G
3N/A
Glycosylation Resources
GlyTouCan: G60087WL
GlyCosmos: G60087WL
GlyGen: G60087WL
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-2)-alpha-L-fucopyranose
H
2N/A
Glycosylation Resources
GlyTouCan: G23386LT
GlyCosmos: G23386LT
GlyGen: G23386LT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.186 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.147 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.21α = 90
b = 80.62β = 90
c = 120.63γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary