4G9N

Crystal structure of the Rhizoctonia solani agglutinin in complex with N'-acetyl-galactosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.154 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural analysis of the Rhizoctonia solani agglutinin reveals a domain-swapping dimeric assembly.

Skamnaki, V.T.Peumans, W.J.Kantsadi, A.L.Cubeta, M.A.Plas, K.Pakala, S.Zographos, S.E.Smagghe, G.Nierman, W.C.Van Damme, E.J.Leonidas, D.D.

(2013) FEBS J 280: 1750-1763

  • DOI: https://doi.org/10.1111/febs.12190
  • Primary Citation of Related Structures:  
    4G9M, 4G9N

  • PubMed Abstract: 

    Rhizoctonia solani agglutinin (RSA) is a 15.5-kDa lectin accumulated in the mycelium and sclerotia of the soil born plant pathogenic fungus R. solani. Although it is considered to serve as a storage protein and is implicated in fungal insecticidal activity, its physiological role remains unclear as a result of a lack of any structure/function relationship information. Glycan arrays showed that RSA displays high selectivity towards terminal nonreducing N-acetylgalactosamine residues. We determined the amino acid sequence of RSA and also determined the crystal structures of the free form and the RSA-N-acetylgalactosamine complex at 1.6 and 2.2 Å resolution, respectively. RSA is a homodimer comprised of two monomers adopting the β-trefoil fold. Each monomer accommodates two different carbohydrate-binding sites in an asymmetric way. Despite RSA topology similarities with R-type lectins, the two-monomer assembly involves an N-terminal swap, thus creating a dimer association novel to R-type lectins. Structural characterization of the two carbohydrate-binding sites offers insights on the structural determinants of the RSA carbohydrate specificity.


  • Organizational Affiliation

    Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
agglutinin
A, B
143Rhizoctonia solaniMutation(s): 0 
UniProt
Find proteins for L8WGI4 (Thanatephorus cucumeris (strain AG1-IA))
Explore L8WGI4 
Go to UniProtKB:  L8WGI4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL8WGI4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.583α = 90
b = 61.251β = 93.45
c = 32.839γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
CrysalisProdata collection
CrysalisProdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary