1ENM

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

• PDB DOI: https://doi.org/10.2210/pdb1ENM/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Urtica dioica
• Mutation(s): Yes 


• Deposited: 2000-03-21 Released: 2000-06-21 
• Deposition Author(s): Saul, F.A., Rovira, P., Boulot, G., Van Damme, E.J.M., Peumans, W.J., Truffa-Bachi, P., Bentley, G.A.

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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 

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

• PubMed: 10873861 
• DOI: https://doi.org/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 Vbeta8.3(+) 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.98 kDa 
• Atom Count: 750 
• Modelled Residue Count: 91 
• Deposited Residue Count: 94 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGGLUTININ ISOLECTIN I/AGGLUTININ ISOLECTIN V/ AGGLUTININ ISOLECTIN VI	A	89	Urtica dioica	Mutation(s): 5
UniProt
Find proteins for P11218 (Urtica dioica) Explore P11218  Go to UniProtKB:  P11218

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	B	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

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 = 38.78	α = 90
b = 46.16	β = 90
c = 57.25	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-06-21 
Deposition Author(s): Saul, F.A., Rovira, P., Boulot, G., Van Damme, E.J.M., Peumans, W.J., Truffa-Bachi, P., Bentley, G.A.

Revision History  

• 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
• Version 3.1: 2023-08-09
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary