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 >> >> <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> >> >> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.facebook.com%2Fproteindatabank&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bPsYJQXaFV05F%2FeeVBASaECt2h13U4HJVNzrfLs2w5k%3D&reserved=0 >> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.facebook.com%2Fproteindatabank&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bPsYJQXaFV05F%2FeeVBASaECt2h13U4HJVNzrfLs2w5k%3D&reserved=0> >> >> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftwitter.com%2FPDBeurope&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mphXsd3vaMR3wlOQ7%2F7p%2FaI3MKG3LPCGSyfVNg%2FCwrg%3D&reserved=0 >> >> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftwitter.com%2FPDBeurope&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mphXsd3vaMR3wlOQ7%2F7p%2FaI3MKG3LPCGSyfVNg%2FCwrg%3D&reserved=0> >> >> >> >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=stAI21mrmOvHtv0R5FcepDeFB8CRDK%2FkbPbf8Ffk3Wo%3D&reserved=0 >> >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=stAI21mrmOvHtv0R5FcepDeFB8CRDK%2FkbPbf8Ffk3Wo%3D&reserved=0 > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=stAI21mrmOvHtv0R5FcepDeFB8CRDK%2FkbPbf8Ffk3Wo%3D&reserved=0 > > This message was issued to members of > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=wDJLwgYIAicmIzlIKZRu4HvhOpq9WjDrYMXXZ8q0arw%3D&reserved=0, > a mailing list hosted by > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ojiT%2B4tYulV15DTAsxNXPy0P7SoESJVtvGx90iOjpTU%3D&reserved=0, > terms & conditions are available at > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=I7zvQYDZlGewc%2BKWOIDt%2FlPZmV%2Fsscc0hydSQDXOqxU%3D&reserved=0 När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s 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, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
