Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

Dale Tronrud Fri, 04 Dec 2020 12:14:43 -0800

I agree that the user experience is very important, but that is notthe purpose of a data base design. The data scheme is designed for thestorage and manipulation of data by software in a clear and unambiguousway. The presentation of the data to a user is the job of theapplication developer, such as yourself. As anyone who has lookedinside a mmCIF will tell you, it was not designed for human reading orediting. Yes, it can be manually edited and read, and that is handy forpeople like you and I, but the average human protein modeler shouldn'tbe in there.

According to Robbie, the information is present in the mmCIF toallow you to code a tool that will allow your users to navigate themodel. Maybe we can discuss off-line ideas for how this can be done.

Anyway, I agree with you that representing glycans with one sugardifferently than poly-glycans is not the best solution. The PDB hasshown little interest in my opinions on such matters in the past so I'mnot getting involved in that argument. I just jumped in to defend theadherence of mmCIF to formal data base theory, and suggest that thesoftware developers reading mmCIF also stick to those rules, and notmake unwarranted assumptions about the meaning of data items.


Dale Tronrud

On 12/4/2020 10:37 AM, Tristan Croll wrote:

OK, I understand your point more clearly now - but I'm not sure I fullyagree, for the simple reason that people aren't computers. You're rightthat for the purposes of software validation tools the chain IDs areessentially arbitrary - as long as they're unique, nothing else reallymatters. But to a human simply wanting to /explore/ a model in theirfavourite visualisation program this makes everything just that bit lessintuitive - if they want to, say, go to the first glycan attached tochain A they have no way of doing so short of tracing through from theN-terminus until they find it, unless the program provides a tool thatalready understands the concept of "first glycan attached to chain A".So if we go forward with the "chain IDs are entirely arbitrary,therefore it doesn't matter what they are" approach, then every existingvisualisation tool gets a little bit more difficult to use with glycansuntil their authors take the time to write new task-specific code.
In the grand scheme of things it's a minor issue, I suppose - but in myopinion it really is important to keep the experience of the end user inmind when making decisions like this.
------------------------------------------------------------------------
*From:* Dale Tronrud <de...@daletronrud.com>
*Sent:* 04 December 2020 18:16
*To:* Tristan Croll <ti...@cam.ac.uk>; CCP4BB@JISCMAIL.AC.UK<CCP4BB@JISCMAIL.AC.UK>*Subject:* Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data atthe PDB -- N-glycans are now separate chains if more than one residue
     Creating meaning in the chain names "A, B, C, Ag1, Ag2, Ag3" is
exactly the problem.  "chain names" ( or "entity identifiers" if I
recall the mmCIF terminology correctly) are simply database "indexes".
The values of indices are meaningless in themselves, they are just
unique values that can be used to unambiguously identify a record. In
principle, you could just assign random ISO characters (I don't think
mmCIF allows unicode) and the mmCIF would be considered identical.

     You are trying to force meaning to the characters with an index, and
that puts multiple types of information in a single field.  As Robbie
said already exists, if you want to encode connectivity into the data
base you have to add records that define that connectivity.  That places
the connectivity information explicitly in the data models and allows
standard data base tools to track and validate.

     The idioms of the PDB cause problems that lead people to these
mistakes.  The PDB assigns the indices "1", "2", and "3" to residues in
a chain.  A person could be misled into thinking that "2" comes between
"1" and "3" in the sequence.  This is not necessarily true at all.  To
learn the sequence you have to go to the mmCIF records that define the
connectivity between residues.  It is entirely possible that "3" comes
before "1" because these indexes don't contain any information, other
than being unique within the chain.

Dale Tronrud

On 12/4/2020 9:46 AM, Tristan Croll wrote:
     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 suggestinganything 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 Acontaining amino acid residues 1-200, and 3 N-linked glycans withresidues numbered, say, 1000-1005, 1020-1026 and 1040-1043 (a fairlycommon approach I've seen taken to the problem in the past, and one I'vetaken myself), then if I understand correctly after remediation we'llhave a model with protein chains A-C and glycan chains D-F. The problemis, unless and until all the available visualisation software updates toautomatically associate chains D-F to chain A based on linkage, the userjust 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 youhave 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 immediatelyaccessible 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 atthe 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, andname them by appending characters to the parent chain ID? Using chain Aas 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
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"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
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; 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
<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
<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
<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
<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
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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
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) 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
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at Rutgers,
The State University of New Jersey and is funded by NIGMS grant U01
CA221216 in collaboration with Complex Carbohydrate Research Center
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at the University of Georgia.
If you have any comments or queries regarding the changes to carbohydrate
representation, please visit the wwPDB website
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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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Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

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