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
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at University
of Georgia, WURCS
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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
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