4I6S | pdb_00004i6s

Structure of RSL mutant W76A in complex with L-fucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 
    0.172 (Depositor), 0.183 (DCC) 
  • R-Value Work: 
    0.148 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.149 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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: 1918-1924

  • DOI: https://doi.org/10.1021/cb400254b
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 31.18 kDa 
  • Atom Count: 2,436 
  • Modeled Residue Count: 266 
  • Deposited Residue Count: 273 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative fucose-binding lectin protein
A, B, C
91Ralstonia solanacearumMutation(s): 1 
Gene Names: CMR15_11270rsc2107

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
K [auth B],
N [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
FUL

Query on FUL



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
M [auth C],
O [auth C]
beta-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
FUC

Query on FUC



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
G [auth B],
H [auth B],
L [auth C]
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
J [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free:  0.172 (Depositor), 0.183 (DCC) 
  • R-Value Work:  0.148 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.149 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.765α = 90
b = 103.765β = 90
c = 100.834γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



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: 2013-09-25
    Changes: Database references
  • Version 1.2: 2013-10-09
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary