This question just seems to come again and again. Search on the web with phenixbb and glycan or mannose, etc. You'll see the answer. I do have a related question to the developers, however. In recent articles published, it was pointed out that 30% of glycoproteins in the pdb had incorrect geometries and names for sugars (Lutteke, Frank, von der Lieth, Carbohydrate Research, 2004; Crispin, Stuart, Jones, NSMB, 2007). The most common error apparently is the alpha mannose having beta geometry, and vice versa. We are also told that beta mannose should have the three-letter code BMA, and alpha mannose is MAN, which is a nice convention to follow. Unfortunately, this convention is not always followed by users, and monomer libraries come with definitions for both alpha and beta anomers called the same three-letter code. The fact that both stereoisomers are found in the same glycosylation chain in all eukaryotes, actually linked to each other, makes an ugly sight. This is like having a polypeptide chain of L-Ala linked to D-Ala, and calling it Ala-Ala, which would cause confusion. Of course, if the person who modeled the structure knows to use the correct cif link, the stereochemistry is correct, but it will not be clear to people looking at the sequence or even at the actual structure; rules for defining anomers are complicated. (Just to make things worse, I don't currently see a BMA.cif in the phenix monomer library, although it is in the list file. Thankfully, there is a MAN-b-D, which one can modify to have a three-letter code of BMA. Or one can use the ccp4 monomer library for a BMA cif file). Would the developers creating the extremely useful monomer libraries be interested in taking into account naming conventions for glycoproteins to help new users avoid confusion and possibly mistakes? There is now software for checking proteoglycan naming and chemistries (Lutteke, von der Lieth, BMC Bionformatics, 2004; Berman, Henrick, Nakamura, Markley, NSMB, 2007), and it would also be great incorporating these into validation tools that come with PHENIX, if possible. Nucleic acids and polypeptides might be special, but glycosylation deserves some attention, too, and I believe PDB now sends you warnings if you are trying to deposit structures with incorrectly modeled glycans. Thanks, Engin On 11/10/09 10:12 AM, Zhou, Tongqing (NIH/VRC) [E] wrote:
Dear All,
I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don’t know how to do the “apply_cif_link’ for the extensions such NAG-NAG, NAG-MAN, MAN-MAN…., any suggestions are appreciated.
Thanks,
Tongqing
*Tongqing Zhou, Ph.D. *
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
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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