Figure 1:Ribbon representation of overall structure of IgG-Fc. Oligosaccharides are represented by sticks.
L-Fucose in structures of IgG-Fc:
reinterpretation of experimental data
Glycosylation of IgG-Fc plays an important role in the activation of the immune system response. Effector functions are modulated by different degrees of deglycosylation of IgG-Fc. However, the geometry of oligosaccharides covalently bound to IgG-Fc does not seem to be in good agreement with electron density in most of the structures deposited in the Protein Data Bank. Our study of correlation between the oligosaccharide geometry, connectivity, and electron density shows several discrepancies, mainly for L-fucose. Revision of refinement of two structures containing the Fc-fragment solved at the highest resolution brings clear evidence for alpha-L-fucosylation instead of beta-L-fucosylation as it was claimed in most of the deposited structures in the Protein Data Bank containing the Fc-fragment, and also in the original structures selected for re-refinement. Our revision refinement results in a decrease in R factors, better agreement with electron density, meaningful contacts, and acceptable geometry of L-fucose.
P. Kolenko, T. Skalova, J. Dohnalek, J. Hasek: L-Fucose in crystal structures of IgG-Fc: Reinterpretation of
experimental data. Collect. Czech. Chem. Commun. 73, 2008, 608-615.
link
Figure 1:Ribbon representation of overall structure of IgG-Fc. Oligosaccharides are represented by sticks.
a) 
b) 
c) 
d) 
e) 
f) 
Figure 2: Typical examples of fucose in structures of IgG-Fc. a) Fucose in the original structure 1L6X, b) fucose of chain
D in the original structure 2DTQ, c) fucose in the structure 1H3X, d) ligand FU4 in the structure 2IWG,
e) alpha-L-6-deoxy-Altrose in the structure 1FC1 instead of fucose, f) residual positive maxima in difference electron density
maps belonging to the not-built structure of oligosaccharides in the structure 1FCC. The figures were prepared with COOT.
a) 
b) 
Figure 3: Fucose (represented by sticks covered by electron density) in re-refined structures.
a) fucose in re-refined structure with original PDB code 1L6X, b) fucose in re-refined structure with original PDB code 2DTQ.
The 2|Fo|-|Fc| electron density (blue, contoured at 1 sigma
above the mean) is displayed in a distance of 0.2 nm from the fucose. The figures were prepared with PYMOL.
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For displaying the structures and maps you may use COOT, CCP4MG, PYMOL, or other molecular graphics programs.
The author gratefully thanks to the Czech and Slovak Crystallographic Association (CSCA, http://www.xray.cz), mainly to Radomir Kuzel, for providing the web space.
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