We also recently encountered this way of coordinates treatment - did not find it useful but just left it as it was (life has other more exciting adventures waiting ...).
I strongly support the solution suggested by Luca, A nice day to all, Jan Dohnalek On Fri, Dec 4, 2020 at 8:48 AM Luca Jovine <luca.jov...@ki.se> wrote: > CC: pdb-l > > Dear Zhijie and Robbie, > > I agree with both of you that the new carbohydrate chain assignment > convention that has been recently adopted by PDB introduces confusion, not > just for PDB-REDO but also - and especially - for end users. > > Could we kindly ask PDB to improve consistency by either assigning a > separate chain to all covalently attached carbohydrates (regardless of > whether one or more residues have been traced), or reverting to the old > system (where N-/O-glycans inherited the same chain ID of the protein to > which they are attached)? The current hybrid solution hardly seems > optimal... > > Best regards, > > Luca > > > On 3 Dec 2020, at 20:17, Robbie Joosten <robbie_joos...@hotmail.com> > wrote: > > > > Dear Zhijie, > > > > In generally I like the treatment of carbohydrates now as branched > polymers. I didn't realise there was an exception. It makes sense for > unlinked carbohydrate ligands, but not for N- or O-glycosylation sites as > these might change during model building or, in my case, carbohydrate > rebuilding in PDB-REDO powered by Coot. Thanks for pointing this out. > > > > Cheers, > > Robbie > > > >> -----Original Message----- > >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Zhijie > Li > >> Sent: Thursday, December 3, 2020 19:52 > >> To: CCP4BB@JISCMAIL.AC.UK > >> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the > >> PDB -- N-glycans are now separate chains if more than one residue > >> > >> Hi all, > >> > >> I was confused when I saw mysterious new glycan chains emerging during > >> PDB deposition and spent quite some time trying to find out what was > >> wrong with my coordinates. Then it occurred to me that a lot of recent > >> structures also had tens of N-glycan chains. Finally I realized that > this > >> phenomenon is a consequence of this PDB policy announced here in July. > >> > >> > >> For future depositors who might also get puzzled, let's put it in a > short > >> sentence: O- and N-glycans are now separate chains if it they contain > more > >> than one residue; single residues remain with the protein chain. > >> > >> > >> > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediation&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684263065%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mBrkCJECFpZyCih4kOCcCvLT1GzQHxD5GD7bZDI9s1s%3D&reserved=0 > >> > >> "Oligosaccharide molecules are classified as a new entity type, > branched, > >> assigned a unique chain ID (_atom_site.auth_asym_id) and a new mmCIF > >> category introduced to define the type of branching > >> (_pdbx_entity_branch.type) . " > >> > >> > >> > >> > >> > >> I found the differential treatment of single-residue glycans and > multi-residue > >> glycans not only bit lack of aesthetics but also misleading. When a > structure > >> contains both NAG-NAG... and single NAG on N-glycosylation sites, it > might > >> be because of lack of density for building more residues, or because > that > >> some of the glycosylation sites are now indeed single NAGs (endoH etc.) > >> while some others are not cleaved due to accessibility issues. > Leaving NAGs > >> on the protein chain while assigning NAG-NAG... to a new chain, feels > like > >> suggesting something about their true oligomeric state. > >> > >> > >> For example, for cryoEM structures, when one only builds a single NAG > at a > >> site does not necessarily mean that the protein was treated by endoH. In > >> fact all sites are extended to at least tri-Man in most cases. Then why > >> keeping some sites associated with the protein chain while others kicked > >> out? > >> > >> Zhijie > >> > >> > >> > >> ________________________________ > >> > >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of John > >> Berrisford <j...@ebi.ac.uk> > >> Sent: Thursday, July 9, 2020 4:39 AM > >> To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > >> Subject: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB > >> > >> > >> Dear CCP4BB > >> > >> PDB data will shortly incorporate a new data representation for > >> carbohydrates in PDB entries and reference data that improves the > >> Findability and Interoperability of these molecules in macromolecular > >> structures. In order to remediate and improve the representation of > >> carbohydrates across the archive, the wwPDB has: > >> > >> *standardized Chemical Component Dictionary nomenclature > >> following IUPAC-IUBMB recommendations > >> *provided uniform representation for oligosaccharides > >> *adopted Glycoscience-community commonly used linear descriptors > >> using community tools > >> *annotated glycosylation sites in PDB structures > >> > >> Starting July 29, 2020, users will be able to access the improved data > via FTP > >> or wwPDB partner websites. Detailed information about this project is > >> available at the wwPDB website > >> < > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediation&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6begIrz7OgNq8CecxMhAhm3n%2F4WPAMM%2F4dg9uwmlrcs%3D&reserved=0> > ; lists > >> of impacted entries and chemical components will be published on this > page > >> after data release. > >> > >> The wwPDB has created a new ‘branched’ entity representation for > >> polysaccharides, describing all the individual monosaccharide > components of > >> these in the PDB entry. As part of this process, we have standardized > atom > >> nomenclature of >1,000 monosaccharides in the Chemical Component > >> Dictionary (CCD) and applied a branched entity representation to > >> oligosaccharides for >8000 PDB entries. To guarantee unambiguous > chemical > >> description of oligosaccharides in the affected PDB entries, an explicit > >> description of covalent linkage information between their monosaccharide > >> units is included. In addition, wwPDB validation reports provide > consistent > >> representation for these oligosaccharides and include 2D representations > >> based on the Symbol Nomenclature for Glycans (SNFG). > >> > >> To support the remediation of carbohydrate representation, software > tools > >> providing linear descriptors were developed in collaboration with the > >> glycoscience community to enable easy translation of PDB data to other > >> representations commonly used by glycobiologists. These include Condense > >> IUPAC from GMML < > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FGLYCAM-Web%2Fgmml&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=eA9rmh0D7QoyPzvwUBC%2BtIgZxdnQ72QWTx74CWQwpWM%3D&reserved=0> > at University > >> of Georgia, WURCS < > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgitlab.com%2Fglyconavi%2Fpdb2glycan&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=TTLXk1QkfdzpSEozxxPuHf58f0EGYjnktH8uNOfoDe0%3D&reserved=0> > from > >> PDB2Glycan at The Noguchi Institute, Japan, and LINUCS > >> < > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.glycosciences.de%2Ftools%2Fpdb2linucs%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=dXclDI7KsaKEajEuBxnbxY%2BjshExxyESN2RKDgJdr%2Fo%3D&reserved=0> > from pdb-care at > >> Germany. > >> > >> Furthermore, to ensure continued Findability of 118 common > >> oligosaccharides (e.g., sucrose, Lewis Y antigen), we have expanded the > >> Biologically Interesting molecule Reference Dictionary (BIRD > >> < > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdata%2Fbird&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=feM%2F6RPoFqQwdIABus%2BD60JSTSbdi2UzsV62IRKX%2Fvg%3D&reserved=0> > ) that contains the covalent linkage > >> information and common synonyms for such molecules. > >> > >> wwPDB has also used this opportunity to improve the organization of > >> chemical synonyms in the CCD by introducing a new > >> _pdbx_chem_comp_synonyms data category. This will enable more > >> comprehensive capture of alternative names for small molecules in the > PDB. > >> To minimize disruption to users, the legacy data item, > >> _chem_comp.pdbx_synonyms, will be retained for a transition period > >> through 2021. > >> > >> The carbohydrate remediation project is a wwPDB collaborative project > that > >> is carried out principally by RCSB PDB < > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rcsb.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=28mQbs4C%2FKygkU5GY1mNYzfX6Y1a76onFlsFwcpsVZU%3D&reserved=0> > at Rutgers, > >> The State University of New Jersey and is funded by NIGMS grant U01 > >> CA221216 in collaboration with Complex Carbohydrate Research Center > >> < > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ccrc.uga.edu%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gkU8DWkdVXFE%2BCjcV2mEbU6I%2FECM5Dlq2XCErqtQEKk%3D&reserved=0> > at the University of Georgia. > >> > >> If you have any comments or queries regarding the changes to > carbohydrate > >> representation, please visit the wwPDB website > >> < > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediation&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6begIrz7OgNq8CecxMhAhm3n%2F4WPAMM%2F4dg9uwmlrcs%3D&reserved=0> > or > >> 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