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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> > *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 <[EMAIL PROTECTED] <[EMAIL PROTECTED]>> > 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)<asn.JPG> > > > > > > > > > -- > Jiamu Du > State Key Laboratory of Molecular Biology > Institute of Biochemistry and Cell Biology Shanghai Institutes for > Biological Sciences > Chinese Academy of Sciences (CAS) > > ------------------------------ > > No virus found in this incoming message. > Checked by AVG Free Edition. > Version: 7.5.516 / Virus Database: 269.17.13/1213 - Release Date: 1/7/2008 > 9:14 AM > > -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)
