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Re: [ccp4bb] how to model this density?
 

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CCP4bb <-- 2008 <-- January 2008 <-- 08 January 2008
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Subject: Re: how to model this density?
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2008-01-08
Thank you all.
I have build a (NAG)2MAN core sugar chain into the density. It seems more
MAN can be fit into the density.


On Jan 9, 2008 5:07 AM, Li Zhijie wrote:

> Hi Jiamu,
>
> I think you can safely say that it is an N-linked glycan.
>
> To model the sugar, check COOT's "get monomer" function. The first sugar
> should be GlcNAc, the 3-letter Code of which is "NAG". If your density also
> shows the second sugar, it is NAG again - make sure to check the glycoside
> linkage between them, which should be beta 1-4. If you still have more
> density to fit, check the N-glycan biosynthesis pathway here:
> http://www.genome.ad.jp/kegg/pathway/map/map00510.html. I think CHO cells
> predominantly produce the complex type N-glycans. CHO cells may also add
> an alpha1,6 fucose to the first GlcNAc.
>
>
> ----- Original Message -----
>
> *From:* Jiamu Du
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Sent:* Monday, January 07, 2008 10:45 PM
> *Subject:* Re: [ccp4bb] how to model this density?
>
> Dear Jeff:
> The sequence here is NYT. I think it is glycosylated here, isn't it?
> Thanks a lot.
>
> On Jan 8, 2008 11:37 AM, Jeff Lee >
> wrote:
>
> > Hi,
> > Do you know what is the protein sequence in this region. If it is
> > glycosylated, it should have a distinctive motif (N-X-S/T). You might have
> > the first NAG attached to the Asn if the motif is there.
> >
> > Jeff
> >
> >
> > On Jan 7, 2008, at 7:19 PM, Jiamu Du wrote:
> >
> > Dear All:
> > I am refining a structure at 2.6 A reslution. The protein is expressed
> > in CHO cell, so it might be glycosylated.
> > While refining an Asn residue as shown in the figure of the attachment,
> > I found some strange density extended beyond the side chain of Asn. The
> > sigma level for the fofc map of the figure in the attachment is as high as
> > 3.0. My protein buffer is Tris and NaCl, and the reservior is PEG and
> > NH4Cl. I believe this is not water mlecules. Considering the residue is
> > Asn, I guess it might be carbohydrate.
> > Is this density like a carbohydrate molecule? How to model this density?
> >
> > Thanks and Happy New Year.
> >
> > --
> > Jiamu Du
> > State Key Laboratory of Molecular Biology
> > Institute of Biochemistry and Cell Biology Shanghai Institutes for
> > Biological Sciences
> > Chinese Academy of Sciences (CAS)
> >
> >
> >
>
>
> --
> Jiamu Du
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology Shanghai Institutes for
> Biological Sciences
> Chinese Academy of Sciences (CAS)
>
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>


--
Jiamu Du
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)
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