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 10:17:01 -0800

Creating meaning in the chain names "A, B, C, Ag1, Ag2, Ag3" isexactly the problem. "chain names" ( or "entity identifiers" if Irecall the mmCIF terminology correctly) are simply database "indexes".The values of indices are meaningless in themselves, they are justunique values that can be used to unambiguously identify a record. Inprinciple, you could just assign random ISO characters (I don't thinkmmCIF allows unicode) and the mmCIF would be considered identical.

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

The idioms of the PDB cause problems that lead people to thesemistakes. The PDB assigns the indices "1", "2", and "3" to residues ina 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. Tolearn the sequence you have to go to the mmCIF records that define theconnectivity between residues. It is entirely possible that "3" comesbefore "1" because these indexes don't contain any information, otherthan 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
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediation&amp;data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684263065%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=mBrkCJECFpZyCih4kOCcCvLT1GzQHxD5GD7bZDI9s1s%3D&amp;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
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wwPDB has also used this opportunity to improve the organization of
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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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