1N47

Isolectin B4 from Vicia villosa in complex with the Tn antigen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The crystal structure of a plant lectin in complex with the Tn antigen

Babino, A.Tello, D.Rojas, A.Bay, S.Osinaga, E.Alzari, P.M.

(2003) FEBS Lett 536: 106-110

  • DOI: 10.1016/s0014-5793(03)00037-1
  • Primary Citation of Related Structures:  
    1N47

  • PubMed Abstract: 
  • The structure of the tetrameric Vicia villosa isolectin B4 (VVLB4) in complex with a cancer antigen, the Tn glycopeptide (GalNAc-O-Ser), was determined at 2.7 A resolution. The N-acetylgalactoside moiety of the ligand binds to the primary combining site of VVLB4 in a similar way as observed for other Gal/GalNAc-specific plant lectins ...

    The structure of the tetrameric Vicia villosa isolectin B4 (VVLB4) in complex with a cancer antigen, the Tn glycopeptide (GalNAc-O-Ser), was determined at 2.7 A resolution. The N-acetylgalactoside moiety of the ligand binds to the primary combining site of VVLB4 in a similar way as observed for other Gal/GalNAc-specific plant lectins. The amino acid moiety of the Tn antigen is largely exposed to the solvent and makes few contacts with the protein. The structure of the complex provides a framework to understand the differences in the strength of VVLB4 binding to different sugars and emphasizes the role of a single protein residue, Tyr127, as a structural determinant of Tn-binding specificity.


    Related Citations: 
    • Amino acid sequence and three-dimensional structure of the Tn-specific isolectin B4 from Vicia villosa.
      Osinaga, E., Tello, D., Batthyany, C., Bianchet, M., Tavares, G., Duran, R., Cervenansky, C., Camoin, L., Roseto, A., Alzari, P.M.
      (1997) FEBS Lett 412: 190

    Organizational Affiliation

    Departamento de Bioquimica, Facultad de Medicina, Av. Gral Flores 2125, Montevideo, Uruguay.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isolectin B4 ABCD233Vicia villosaMutation(s): 0 
Find proteins for P56625 (Vicia villosa)
Explore P56625 
Go to UniProtKB:  P56625
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.51α = 90
b = 85.51β = 90
c = 153.65γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary