3C9Z

Sambucus nigra agglutinin II (SNA-II), tetragonal crystal form

Summary for 3C9Z

• Entry DOI: 10.2210/pdb3c9z/pdb
• Related: 3CA0 3CA1 3CA3 3CA4 3CA5 3CA6 3CAH
• Descriptor: Agglutinin II, alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (7 entities in total)
• Functional Keywords: beta-trefoil, ricin-b domain, glycosylation, glycoprotein, lectin, sugar binding protein, plant protein
• Biological source: Sambucus nigra (European elder, elderberry)
• Total number of polymer chains: 1
• Total formula weight: 30669.05

Authors

Maveyraud, L.,Guillet, V.,Mourey, L. (deposition date: 2008-02-19, release date: 2008-11-25, Last modification date: 2024-10-30)

Primary citation

Maveyraud, L.,Niwa, H.,Guillet, V.,Svergun, D.I.,Konarev, P.V.,Palmer, R.A.,Peumans, W.J.,Rouge, P.,Van Damme, E.J.,Reynolds, C.D.,Mourey, L.
Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra
Proteins, 75:89-103, 2009

PubMed Abstract: Bark of elderberry (Sambucus nigra) contains a galactose (Gal)/N-acetylgalactosamine (GalNAc)-specific lectin (SNA-II) corresponding to slightly truncated B-chains of a genuine Type-II ribosome-inactivating protein (Type-II RIPs, SNA-V), found in the same species. The three-dimensional X-ray structure of SNA-II has been determined in two distinct crystal forms, hexagonal and tetragonal, at 1.90 A and 1.35 A, respectively. In both crystal forms, the SNA-II molecule folds into two linked beta-trefoil domains, with an overall conformation similar to that of the B-chains of ricin and other Type-II RIPs. Glycosylation is observed at four sites along the polypeptide chain, accounting for 14 saccharide units. The high-resolution structures of SNA-II in complex with Gal and five Gal-related saccharides (GalNAc, lactose, alpha1-methylgalactose, fucose, and the carcinoma-specific Tn antigen) were determined at 1.55 A resolution or better. Binding is observed in two saccharide-binding sites for most of the sugars: a conserved aspartate residue interacts simultaneously with the O3 and O4 atoms of saccharides. In one of the binding sites, additional interactions with the protein involve the O6 atom. Analytical gel filtration, small angle X-ray scattering studies and crystal packing analysis indicate that, although some oligomeric species are present, the monomeric species predominate in solution.

PubMed: 18798567
DOI: 10.1002/prot.22222

Experimental method

X-RAY DIFFRACTION (1.35 Å)