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://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 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/
