3ZI8

Structure of the R17A mutant of the Ralstonia soleanacerum lectin at 1.5 Angstrom in complex with L-fucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Reduction of Lectin Valency Drastically Changes Glycolipid Dynamics in Membranes, But not Surface Avidity.

Arnaud, J.Claudinon, J.Trondle, K.Trovaslet, M.Larson, G.Thomas, A.Varrot, A.Romer, W.Imberty, A.Audfray, A.

(2013) ACS Chem Biol 8: 1918

  • DOI: https://doi.org/10.1021/cb400254b
  • Primary Citation of Related Structures:  
    3ZI8, 4I6S

  • PubMed Abstract: 

    Multivalency is proposed to play a role in the strong avidity of lectins for glycosylated cell surfaces and also in their ability to affect membrane dynamics by clustering glycosphingolipids. Lectins with modified valency were designed from the β-propeller fold of Ralstonia solanacearum lectin (RSL) that presents six fucose binding sites. After identification of key amino acids by molecular dynamics calculations, two mutants with reduced valency were produced. Isothermal titration calorimetry confirmed the loss of three high affinity binding sites for both mutants. Crystal structures indicated that residual low affinity binding occurred in W76A but not in R17A. The trivalent R17A mutant presented unchanged avidity toward fucosylated surfaces, when compared to hexavalent RSL. However, R17A is not able anymore to induce formation of membrane invaginations on giant unilamellar vesicules, indicating the crucial role of number of binding sites for clustering of glycolipids. In the human lung epithelial cell line H1299, wt-RSL is internalized within seconds whereas the kinetics of R17A uptake is largely delayed. Neolectins with tailored valency are promising tools to study membrane dynamics.


  • Organizational Affiliation

    CERMAV-CNRS (affiliated to Grenoble Université and ICMG), BP53, 38041 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE FUCOSE-BINDING LECTIN PROTEIN90Ralstonia solanacearumMutation(s): 1 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.399α = 90
b = 72.399β = 90
c = 35.99γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Data collection, Structure summary
  • Version 2.0: 2017-11-29
    Changes: Advisory, Atomic model, Non-polymer description, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 2.2: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary