[phenixbb] NAG-NAG description

Engin Ozkan eozkan at stanford.edu
Wed Jun 2 12:47:30 PDT 2010

  If you look up glycobiology textbooks, you can find a general scheme 
for insects. Check out the free book Essentials in Glycobiology on 
NCBI's Books collection. I am sure you can also find more on 
lepidopteran cell lines (such as Sf9, High five).

shows you how it is in insects and other main taxa.

To summarize, for insects in general, I would expect this:

             | |                        |
(alpha1,3)FUC (alpha1,6)FUC         (alpha1,6)MAN

Hope this helps a little. Most people are surprised to find the fucose 
on the C3 of the first NAG, because that does not appear in mammals, but 
can in insects. I am sure experts can chime in more.


On 6/2/10 12:27 PM, Chris Ulens wrote:
> As a follow-up on the NAG-NAG question I was wondering if other insect 
> cell users could point me to the proper sources in the literature that 
> describe the most common glycosylation forms in Sf9/Sf21 insect cells. 
> It seems we have chains composed of up to 4 sugar molecules attached 
> to an Asn residue and it would be helpful to know which sugars are 
> most likely to follow after NAG-NAG.
> Thanks.
> -Chris
> On Jun 1, 2010, at 1:44 PM, Chris Ulens wrote:
> Thanks for the feedback.
> I would like to refine a NAG-NAG chain attached to residue Asn122 in
> my structure. There are 5 identical subunits.
> Could you verify my .params file?
> I get the following error:
> Empty atom selection
> refinement
> .pdb_interpretation.apply_cif_link.residue_selection_1="chain A and
> resname NAG and resid 122"
> Thanks.
> -Chris
> <cif_link1.params><ATT00001..txt><ATT00002..txt>
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Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111

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