Yes Tristan, that would be even better - also because such an Ag1, Ag2,… system could conveniently fall back on a single-character chain A, when generating legacy PDB format files from the mmCIF ones. Exactly for the reason that you pointed out, personally I do not understand the logic of assigning a different chain ID to covalently attached glycans (or any other covalent post-translational modification, for that matter). Aren't residue IDs enough to make it clear that such residues are not amino acids? -Luca
> On 4 Dec 2020, at 09:06, Tristan Croll <ti...@cam.ac.uk> 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> 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%7Ca3fed8eed9d94a481d6808d8982b731f%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426659666244613%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=BqPiPeexG0nLhUmaih2Bq8ppjkX%2F%2BbLP4SoBGL4u5%2Fw%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%7Ca3fed8eed9d94a481d6808d8982b731f%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426659666244613%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=BqPiPeexG0nLhUmaih2Bq8ppjkX%2F%2BbLP4SoBGL4u5%2Fw%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%7Ca3fed8eed9d94a481d6808d8982b731f%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426659666254569%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ZfvfU%2FBudQysETQjHkvR3NPuF8AWyGaNJ%2BirouL23BA%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%7Ca3fed8eed9d94a481d6808d8982b731f%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426659666254569%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=8FaXeDf8Hk%2BUB1BVsGRm4KL6ALdDEtS1HGbik28T1%2B8%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%7Ca3fed8eed9d94a481d6808d8982b731f%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426659666254569%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=qGJLV%2FzVgdyGcUQNDKOYIlPiyKn6z9P7E5j7G8tatRk%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%7Ca3fed8eed9d94a481d6808d8982b731f%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426659666254569%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=1pqguhV4s5Ajh1ctx0CDE0zNSefDGK8qwQl9lky%2BSPs%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%7Ca3fed8eed9d94a481d6808d8982b731f%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426659666254569%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Y2%2BaEG2JioqaVYp8Q0Mpq0f8yzraA5Jnehsi0kjhsaE%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%7Ca3fed8eed9d94a481d6808d8982b731f%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426659666254569%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=K9KewAawbZOOuPMgKdNDk78U%2BkjNQD1YPqiJyxwkhZU%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%7Ca3fed8eed9d94a481d6808d8982b731f%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426659666254569%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Nzc%2BaBH%2BBz0DpAMUn50DtqqBMCKrlmysYxJqTlMlcPA%3D&reserved=0> >>>> or >>>> 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