Dear Dale and Robbie, I agree with your comments! But may I stir back the discussion to the original issue, which is that one-residue N-glycans are now treated differently from multi-residue N-glycans (although they are both covalently linked to a protein chain)? This inconsistency is independent of the file format…
Best, Luca On 4 Dec 2020, at 18:30, Robbie Joosten <robbie_joos...@hotmail.com<mailto:robbie_joos...@hotmail.com>> wrote: Dear Dale, Yes, good point. Let's stop bending over backwards to come up with faux PDB compatibility and focus on making mmCIF better. There are struct_conn records that describe the linkages. This is enough to reconstruct the connectivity. There is an ongoing debate on how to capture the restraints for such linkages. But at least this can in principle be captured in mmCIF whereas this is pretty much undoable in PDB format. Cheers, Robbie On 4 Dec 2020 18:01, Dale Tronrud <de...@daletronrud.com<mailto:de...@daletronrud.com>> wrote: This suggestion violates a basic principle of data base theory. A single data item cannot encode two pieces of information. The whole structure of CIF falls apart if this is done. Does the new PDB convention contain a CIF record of the link that bridges between the protein chain and the, now separated, glycan chain? If not, I think this is the principle failing of their new scheme. Dale Tronrud On 12/4/2020 12:06 AM, Tristan Croll wrote: > 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<mailto: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<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Zhijie >>>> Li >>>> Sent: Thursday, December 3, 2020 19:52 >>>> To: CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of John >>>> Berrisford <j...@ebi.ac.uk<mailto:j...@ebi.ac.uk>> >>>> Sent: Thursday, July 9, 2020 4:39 AM >>>> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> >>>> <CCP4BB@JISCMAIL.AC.UK<mailto: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 >>>> contact us at >>>> deposit-h...@mail.wwpdb.org<mailto:deposit-h...@mail.wwpdb.org> >>>> <mailto:deposit- >>>> h...@mail.wwpdb.org<mailto:h...@mail.wwpdb.org>> . >>>> >>>> >>>> >>>> >>>> >>>> Regards >>>> >>>> >>>> >>>> John >>>> >>>> >>>> >>>> -- >>>> >>>> John Berrisford >>>> >>>> PDBe >>>> >>>> European Bioinformatics Institute (EMBL-EBI) >>>> >>>> European Molecular Biology Laboratory >>>> >>>> Wellcome Trust Genome Campus >>>> >>>> Hinxton >>>> >>>> Cambridge CB10 1SD UK >>>> >>>> Tel: +44 1223 492529 >>>> >>>> >>>> >>>> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pdbe.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jtQQunJvDpFvpPIo3b%2BgX0ETtF5TeAvPE07SMtoClQs%3D&reserved=0 >>>> >>>> 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