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://www.wwpdb.org/documentation/carbohydrate-remediation > > "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://www.wwpdb.org/documentation/carbohydrate-remediation> ; 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://github.com/GLYCAM-Web/gmml> at University > of Georgia, WURCS <https://gitlab.com/glyconavi/pdb2glycan> from > PDB2Glycan at The Noguchi Institute, Japan, and LINUCS > <http://www.glycosciences.de/tools/pdb2linucs/> 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://www.wwpdb.org/data/bird> ) 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://www.rcsb.org/> at Rutgers, > The State University of New Jersey and is funded by NIGMS grant U01 > CA221216 in collaboration with Complex Carbohydrate Research Center > <https://www.ccrc.uga.edu/> at the University of Georgia. > > If you have any comments or queries regarding the changes to carbohydrate > representation, please visit the wwPDB website > <https://www.wwpdb.org/documentation/carbohydrate-remediation> 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 > > > > http://www.pdbe.org <http://www.pdbe.org/> > > http://www.facebook.com/proteindatabank > <http://www.facebook.com/proteindatabank> > > http://twitter.com/PDBeurope <http://twitter.com/PDBeurope> > > > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
