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Lectin(agglutinin) PDB id
2cwg
Jmol
Contents
Protein chains
171 a.a. *
Ligands
ASP-THR-TYR-ALA-
ALA-THR-PRO-ARG
ALA-THR-PRO
SIA-GAL-NDG-SIA ×2
Waters ×389
* Residue conservation analysis
PDB id:
2cwg
Name: Lectin(agglutinin)
Title: Crystallographic refinement and structure analysis of the complex of wheat germ agglutinin with a bivalent sialoglycopeptide from glycophorin a
Structure: Agglutinin isolectin 1 (wga1). Chain: a, b. T5 sialoglycopeptide of glycophorin a. Chain: d, e. Engineered: yes
Source: Triticum aestivum. Bread wheat. Organism_taxid: 4565.
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.171    
Authors: C.S.Wright
Key ref: C.S.Wright and J.Jaeger (1993). Crystallographic refinement and structure analysis of the complex of wheat germ agglutinin with a bivalent sialoglycopeptide from glycophorin A. J Mol Biol, 232, 620-638. PubMed id: 8345526 DOI: 10.1006/jmbi.1993.1415
Date:
08-Jan-93     Release date:   31-Jan-94    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P10968  (AGI1_WHEAT) -  Agglutinin isolectin 1
Seq:
Struc: 		212 a.a.
171 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cell wall macromolecule catabolic process   2 terms 
  Biochemical function     sugar binding     3 terms  

 

 
DOI no: 10.1006/jmbi.1993.1415 J Mol Biol 232:620-638 (1993)
PubMed id: 8345526  
 
 
Crystallographic refinement and structure analysis of the complex of wheat germ agglutinin with a bivalent sialoglycopeptide from glycophorin A.
C.S.Wright, J.Jaeger.
 
  ABSTRACT  
 
Wheat germ agglutinin (WGA) elicits a number of biological effects in erythrocytes as a result of specific binding to the transmembrane protein glycophorin A. The structure of co-crystals of WGA (isolectin 1: WGA1) with a bivalent sialoglycopeptide fragment of glycophorin A (T5), determined at 2.0 A resolution, has been further refined and analyzed with respect to ligand-induced changes in the tertiary structure, mobility, solvation, saccharide conformation and protein/saccharide interactions at three independent N-acetyl-D-neuraminic (NeuNAc) binding sites. The final model, which includes the two independent WGA1 monomers (composed of domains A, B, C and D), two positions for bound T5 sialo-tetrasaccharide (NeuNAc-alpha 2,3-Gal-beta 1,3-(alpha 2,6-NeuNAc)GalNAc) and 386 water molecules, refined to a crystallographic R-factor of 17.1% (Fo > 1.0 sigma) and an average temperature factor of 31.99 A2. Comparisons between the tertiary structures of the liganded and unliganded WGA1 dimers indicate that the largest deviations from 2-fold symmetry are localized in domains engaged in sugar binding (B1 and C2) and at the C-terminal domain of monomer II (D2), forming a strong lattice contact. Interactions of the tetrasaccharide with amino acid ligands in the three binding sites and with water were carefully analyzed and compared. Bound conformations of terminal NeuNAc match to within a root-mean-square delta r of 0.3 A. The specificity-determining N-acetyl group superimposes best in comparison with other substituents of the sugar ring. Of the five domain binding sites that are not occupied in this dimeric crosslinked complex, only one is accessible to the NeuNAc monosaccharide as determined from a difference Fourier map at 3.0 A resolution.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
15229884 E.S.Shih, and M.J.Hwang (2004).
Alternative alignments from comparison of protein structures.
  Proteins, 56, 519-527.  
15340924 K.B.Murray, W.R.Taylor, and J.M.Thornton (2004).
Toward the detection and validation of repeats in protein structure.
  Proteins, 57, 365-380.  
15039554 T.Fujii, M.Hayashida, M.Hamasu, M.Ishiguro, and Y.Hata (2004).
Structures of two lectins from the roots of pokeweed (Phytolacca americana).
  Acta Crystallogr D Biol Crystallogr, 60, 665-673.
PDB codes: 1uha 1uln
11874467 D.Neumann, O.Kohlbacher, H.P.Lenhof, and C.M.Lehr (2002).
Lectin-sugar interaction. Calculated versus experimental binding energies.
  Eur J Biochem, 269, 1518-1524.  
11786557 L.J.Olson, J.Zhang, N.M.Dahms, and J.J.Kim (2002).
Twists and turns of the cation-dependent mannose 6-phosphate receptor. Ligand-bound versus ligand-free receptor.
  J Biol Chem, 277, 10156-10161.
PDB code: 1keo
12181064 M.C.Brain, J.M.Prevost, C.E.Pihl, and C.B.Brown (2002).
Glycophorin A-mediated haemolysis of normal human erythrocytes: evidence for antigen aggregation in the pathogenesis of immune haemolysis.
  Br J Haematol, 118, 899-908.  
11562490 Y.Ha, D.J.Stevens, J.J.Skehel, and D.C.Wiley (2001).
X-ray structures of H5 avian and H9 swine influenza virus hemagglutinins bound to avian and human receptor analogs.
  Proc Natl Acad Sci U S A, 98, 11181-11186.
PDB codes: 1jsh 1jsi 1jsn 1jso
  10873861 F.A.Saul, P.Rovira, G.Boulot, E.J.Damme, W.J.Peumans, P.Truffa-Bachi, and G.A.Bentley (2000).
Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II.
  Structure, 8, 593-603.
PDB codes: 1eis 1en2 1enm
10217149 A.Tulp, D.Verwoerd, and J.Neefjes (1999).
Lectin-induced retardation of subcellular organelles during preparative density gradient electrophoresis: selective purification of plasma membranes.
  Electrophoresis, 20, 438-444.  
10393293 S.D.Wood, L.M.Wright, C.D.Reynolds, P.J.Rizkallah, A.K.Allen, W.J.Peumans, and E.J.Van Damme (1999).
Structure of the native (unligated) mannose-specific bulb lectin from Scilla campanulata (bluebell) at 1.7 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 1264-1272.
PDB code: 1b2p
9305654 T.Stehle, and S.C.Harrison (1997).
High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding.
  EMBO J, 16, 5139-5148.
PDB codes: 1vpn 1vps
  8844838 C.S.Wright, and G.E.Kellogg (1996).
Differences in hydropathic properties of ligand binding at four independent sites in wheat germ agglutinin-oligosaccharide crystal complexes.
  Protein Sci, 5, 1466-1476.  
7588755 H.Nagahora, K.Harata, M.Muraki, and Y.Jigami (1995).
Site-directed mutagenesis and sugar-binding properties of the wheat germ agglutinin mutants Tyr73Phe and Phe116Tyr.
  Eur J Biochem, 233, 27-34.  
7620327 J.J.Ramsden, and C.S.Wright (1995).
The interaction between wheat germ agglutinin and membrane incorporated glycophorin A. An optical binding study.
  Glycoconj J, 12, 113-121.  
8574697 J.M.Rini (1995).
X-ray crystal structures of animal lectins.
  Curr Opin Struct Biol, 5, 617-621.  
7664103 K.Drickamer (1995).
Multiplicity of lectin-carbohydrate interactions.
  Nat Struct Biol, 2, 437-439.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.