1ENM

UDA TRISACCHARIDE COMPLEX. CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ, A SUPERANTIGEN PRESENTED BY MHC MOLECULES OF CLASS I AND CLASS II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II.

Saul, F.A.Rovira, P.Boulot, G.Van Damme, E.J.M.Peumans, W.J.Truffa-Bachi, P.Bentley, G.A.

(2000) Structure 8: 593-603

  • DOI: 10.1016/s0969-2126(00)00142-8
  • Primary Citation of Related Structures:  
    1EIS, 1EN2, 1ENM

  • PubMed Abstract: 
  • Urtica dioica agglutinin (UDA), a monomeric lectin extracted from stinging nettle rhizomes, is specific for saccharides containing N-acetylglucosamine (GlcNAc). The lectin behaves as a superantigen for murine T cells, inducing the exclusive proliferation of Vbeta8 ...

    Urtica dioica agglutinin (UDA), a monomeric lectin extracted from stinging nettle rhizomes, is specific for saccharides containing N-acetylglucosamine (GlcNAc). The lectin behaves as a superantigen for murine T cells, inducing the exclusive proliferation of Vbeta8.3(+) lymphocytes. UDA is unique among known T cell superantigens because it can be presented by major histocompatibility complex (MHC) molecules of both class I and II.


    Related Citations: 
    • Characterisation of Urtica dioica Agglutinin Isolectins and the Encoding Gene Family
      Does, M.P., Ng, D.K., Dekker, H.L., Peumans, W.J., Houterman, P.M., Van Damme, E.J., Cornelissen, B.J.C.
      (1999) Plant Mol Biol 39: 335

    Organizational Affiliation

    Unité d'Immunologie Structurale (CNRS URA 2185), Institut Pasteur, Paris, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AGGLUTININ ISOLECTIN I/AGGLUTININ ISOLECTIN V/ AGGLUTININ ISOLECTIN VIA89Urtica dioicaMutation(s): 5 
Gene Names: UDA1
EC: 3.2.1.14
UniProt
Find proteins for P11218 (Urtica dioica)
Explore P11218 
Go to UniProtKB:  P11218
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900017
Query on PRD_900017
Btriacetyl-beta-chitotrioseOligosaccharide /  Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.78α = 90
b = 46.16β = 90
c = 57.25γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Advisory, Database references, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary