Hi Tristan, I fully subscribe to your idea! I was quite surprised to see our model revised with different glycan chain IDs upon PDB annotation. I imagine there must have been some "administrative" reasoning behind this decision, but it's just a nightmare for subsequent visualisation. And, to me at least, this change makes no sense. Protein chains with covalently attached glycans are one biochemical, structural and functional unit.
Best wishes, Radu > This suggestion violates a basic principle of data base theory. A > single data item cannot encode two pieces of information. > > I'm sorry if I was unclear, but I don't believe I was suggesting anything of > the sort. Hopefully this example should make it more clear - I'm just > suggesting a slight variation on the existing system, no more: > > If we start with model containing 3 protein chains A-C, with chain A > containing amino acid residues 1-200, and 3 N-linked glycans with residues > numbered, say, 1000-1005, 1020-1026 and 1040-1043 (a fairly common approach > I've seen taken to the problem in the past, and one I've taken myself), then > if I understand correctly after remediation we'll have a model with protein > chains A-C and glycan chains D-F. The problem is, unless and until all the > available visualisation software updates to automatically associate chains D-F > to chain A based on linkage, the user just has to remember that chains D-F are > actually the chain A glycans. This is a simple case, but things quickly become > far more messy when you have multiple glycosylated species each with multiple > glycans per chain. If, instead, the new chain assignments were something like > "A, B, C, Ag1, Ag2, Ag3", then we have something that is far more immediately > accessible to the user. > > ________________________________ > From: Dale Tronrud <de...@daletronrud.com> > Sent: 04 December 2020 17:01 > To: Tristan Croll <ti...@cam.ac.uk>; CCP4BB@JISCMAIL.AC.UK > <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 > > > 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> 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 >>>>> contact us at deposit-h...@mail.wwpdb.org <mailto:deposit- >>>>> 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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You can read more about KIs processing of personal >>> data here<https://ki.se/en/staff/data-protection-policy>. >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> This message was issued to members of >>> www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list >>> hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions >>> are available at https://www.jiscmail.ac.uk/policyandsecurity/ >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of >> www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list >> hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions >> are available at https://www.jiscmail.ac.uk/policyandsecurity/ >> > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > -- Radu Aricescu MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. tel: +44-(0)1223-267049 fax: +44-(0)1223-268305 www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
