PDBsum entry 3c9z

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Sugar binding protein, plant protein PDB id
Protein chain
257 a.a. *
SO4 ×4
Waters ×245
* Residue conservation analysis
PDB id:
Name: Sugar binding protein, plant protein
Title: Sambucus nigra agglutinin ii (sna-ii), tetragonal crystal fo
Structure: Agglutinin ii. Chain: a. Synonym: sna-ii
Source: Sambucus nigra. European elder, elderberry. Tissue: bark
1.35Å     R-factor:   0.162     R-free:   0.200
Authors: L.Maveyraud,V.Guillet,L.Mourey
Key ref:
L.Maveyraud et al. (2008). Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra. Proteins, 75, 89. PubMed id: 18798567 DOI: 10.1002/prot.22222
19-Feb-08     Release date:   25-Nov-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P33183  (NIGB_SAMNI) -  Nigrin b
563 a.a.
257 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - rRNA N-glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.


DOI no: 10.1002/prot.22222 Proteins 75:89 (2008)
PubMed id: 18798567  
Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra.
L.Maveyraud, H.Niwa, V.Guillet, D.I.Svergun, P.V.Konarev, R.A.Palmer, W.J.Peumans, P.Rougé, E.J.Van Damme, C.D.Reynolds, L.Mourey.
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 betabeta-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, alphaalpha1-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. Proteins 2009. (c) 2008 Wiley-Liss, Inc.
  Selected figure(s)  
Figure 1.
Figure 1. Ribbon representation of the structure of SNA-II. (a) Stereoview of the overall structure of SNA-II colored from blue (N terminus) to red (C terminus) as observed in the hexagonal crystal form. The four glycosylation sites are labeled, and the glycans are represented as pink sticks. Disulphide bridges are represented as sticks. (b) View of Domains I (top) and II (bottom) in two orthogonal orientations. In each domain, subdomains are colored in red, in green, and in blue. The first and fourth -strands of each subdomain forming the central -barrel are indicated with vivid colors. Glycosylation sites and saccharide-binding residues are labeled and represented as sticks. Glycans are represented as pink sticks.
Figure 4.
Figure 4. X-ray analysis of saccharide binding to SNA-II. (a) Stereoview of the saccharide-binding sites of Domain I (top) and of Domain II (bottom), with bound galactose (pink). Saccharide-binding residues are labeled, and water molecules are indicated with a red sphere. Hydrogen bonds are represented with dotted lines. (b) Comparison of the binding of the different saccharides used in this study (pink), except galactose, in the saccharide-binding site of Domain I. The orientation is identical as in (a).
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 75, 89) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21514389 J.P.Yang, X.X.Ma, Y.X.He, W.F.Li, Y.Kang, R.Bao, Y.Chen, and C.Z.Zhou (2011).
Crystal structure of the 30K protein from the silkworm Bombyx mori reveals a new member of the β-trefoil superfamily.
  J Struct Biol, 175, 97.
PDB code: 3pub
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