[phenixbb] NAG-NAG description

[Engin Ozkan]

  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).

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=glyco2&part=ch19&rendertype=figure&id=ch19.f2
shows you how it is in insects and other main taxa.

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

  ASN-(beta1)NAG-(beta1,4)NAG-(beta1,4)BMA-(alpha1,3)MAN
             | |                        |
(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.

Engin


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