2X2T | pdb_00002x2t

CRYSTAL STRUCTURE OF SCLEROTINIA SCLEROTIORUM AGGLUTININ SSA in complex with Gal-beta1,3-Galnac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.195 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.163 (Depositor) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

Literature

Crystal Structure of the Galnac/Gal-Specific Agglutinin from the Phytopathogenic Ascomycete Sclerotinia Sclerotiorum Reveals Novel Adaptation of a Beta-Trefoil Domain

Sulzenbacher, G.Roig-Zamboni, V.Peumans, W.J.Rouge, P.Van Damme, E.J.M.Bourne, Y.

(2010) J Mol Biology 400: 715

  • DOI: https://doi.org/10.1016/j.jmb.2010.05.038
  • Primary Citation Related Structures: 
    2X2S, 2X2T

  • PubMed Abstract: 

    A lectin from the phytopathogenic ascomycete Sclerotinia sclerotiorum that shares only weak sequence similarity with characterized fungal lectins has recently been identified. S. sclerotiorum agglutinin (SSA) is a homodimeric protein consisting of two identical subunits of approximately 17 kDa and displays specificity primarily towards Gal/GalNAc. Glycan array screening indicates that SSA readily interacts with Gal/GalNAc-bearing glycan chains. The crystal structures of SSA in the ligand-free form and in complex with the Gal-beta1,3-GalNAc (T-antigen) disaccharide have been determined at 1.6 and 1.97 A resolution, respectively. SSA adopts a beta-trefoil domain as previously identified for other carbohydrate-binding proteins of the ricin B-like lectin superfamily and accommodates terminal non-reducing galactosyl and N-acetylgalactosaminyl glycans. Unlike other structurally related lectins, SSA contains a single carbohydrate-binding site at site alpha. SSA reveals a novel dimeric assembly markedly dissimilar to those described earlier for ricin-type lectins. The present structure exemplifies the adaptability of the beta-trefoil domain in the evolution of fungal lectins.


  • Organizational Affiliation
    • Architecture et Fonction des Macromolécules Biologiques UMR-6098 CNRS, Université Aix-Marseille, Campus Luminy, Case 932, F-13288 Marseille cedex 09, France.

Macromolecule Content 

  • Total Structure Weight: 17.91 kDa 
  • Atom Count: 1,467 
  • Modeled Residue Count: 152 
  • Deposited Residue Count: 153 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AGGLUTININ153Sclerotinia sclerotiorumMutation(s): 0 
UniProt
Find proteins for A7XUK7 (Sclerotinia sclerotiorum)
Explore A7XUK7 
Go to UniProtKB:  A7XUK7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7XUK7
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G01534TU
GlyCosmos: G01534TU
GlyGen: G01534TU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.195 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.163 (Depositor) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.458α = 90
b = 51.458β = 90
c = 295.987γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, 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: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary