To go one step further: in large, heavily glycosylated multi-chain complexes the assignment of a random new chain ID to each glycan will lead to headaches for people building visualisations using existing viewers, because it loses the easy name-based association of glycan to parent protein chain. A suggestion: why not take full advantage of the mmCIF capability for multi-character chain IDs, and name them by appending characters to the parent chain ID? Using chain A as an example, perhaps the glycans could become Ag1, Ag2, etc.?
> On 4 Dec 2020, at 07:48, 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 >>> 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