pdb-l: Errors in "author determined" bio assy?

Eric Martz emartz at microbio.umass.edu
Sat Jun 15 14:00:58 PDT 2013


Thanks, Roland, for your authoritative observations! I certainly 
agree that these common errors in REMARK 350/biological assembly (BA) 
are unnecessary, and that they are burdensome since the BA is what is 
shown at RSCB (a good idea in principle). I agree that any mechanism 
to improve communication during deposition and avoid these misakes is 
worthwhile. I especially like your proposal that authors should be 
required to submit a statement explaining the basis for the BA 
specified in the deposited entry -- and I think their statement 
should be included in the final public entry. This would surely go a 
long way towards improving the currently regrettable situation.

Eric

At 6/14/13, Dunbrack, Roland wrote:
>This is a really common problem -- authors saying one thing in their 
>paper and depositing a different biological assembly in the PDB. 
>Usually they just deposit the asymmetric unit as their biological 
>assembly in these cases. Example 3pc2 is a dimer in the paper but a 
>monomer in the asymmetric unit and the authors' biological assembly. 
>I have seen cases where the title of the PDB entry says the protein 
>is a tetramer but the author biological assembly is a dimer.
>
>I have brought this up at the RCSB's Advisory Board meetings, and we 
>have had much discussion. It's my understanding that if there is an 
>"author" biological assembly then the authors actually had to send a 
>file at some point during the process. It cannot be that they forgot 
>and the PDB put in the asymmetric unit by default. In this case (at 
>least for entries in the last few years), the PDB would use the PISA 
>biological assembly instead. In a few cases that I have asked 
>specifically about, where the author BA is the same as the 
>asymmetric unit but the paper is different, the PDB checked their 
>records and they had an email exchange with the authors asking "Is 
>the biological assembly the same as the asymmetric unit?" and the 
>authors wrote back "yes."
>
>In our analysis of available annotations (author and PISA), the 
>biological assembly is different from the asymmetric MORE THAN 50% 
>of the time (about half of these cases, it is bigger than the 
>asymmetric unit and about half the time it is smaller). The idea 
>that there is any biological meaning to the asymmetric unit per se 
>is unwarranted.  The biological assembly is one of the very few 
>pieces of information that is deposited with a structure that is not 
>the direct result of the crystallographic experiment. It is the 
>first image you see when you go to a PDB entry page, and it is very 
>important for many purposes. It is critical to get it right and 
>these kinds of mistakes are unnecessary and problematic.
>
>The problem is one of communication between the authors and the PDB. 
>One recent improvement, which I think is operating now, is that the 
>authors are now shown the PISA biological assembly choices and can 
>pick from one of those (often PISA has more than one possible assembly).
>
>I had one idea that the PDB has not yet adopted and I would like to 
>know what crystallographers think of it: I want the PDB to collect a 
>statement from the authors on why they think the biological assembly 
>that they deposit is the correct assembly.
>
>Authors often do have experimental data on the size of the assembly 
>(e.g. AUC) or even better mutational data or other experiments on 
>the interface(s) that are present in the biological assembly in 
>solution. They may have multiple crystal forms of the protein and 
>see the same assembly in more than one crystal form (we and others 
>have used this as evidence in favor of the biological relevance of 
>interfaces in crystals). Or they may be aware of other proteins in 
>the same family that have the same assembly in their crystal 
>structures in the PDB and by inference, if the same assembly is 
>present in the new structure, it is also likely to be biological. In 
>some cases, it may be simply hypothetical and that would be fine. It 
>would be nice to know if the deposited assembly is only a guess.
>
>I think this annotation is especially important when no paper is 
>published but even when it is, it might deter these kinds of mistakes.
>
>What do you think?
>
>Roland
>
>---------------------------------
>Roland Dunbrack
>Professor, Institute for Cancer Research
>Fox Chase Cancer Center
>Philadelphia PA 19111
>http://dunbrack.fccc.edu
>http://dunbrack.org
>
>
>On 06/13/2013 10:39 PM, Eric Martz wrote:
> > It is my impression that when the "author determined" biological
> > assembly (REMARK 350) specifies the same structure as the asymmetric
> > unit, sometimes the authors simply forgot to specify a known assembly
> > during PDB deposition. Does anyone know of PDB entries where this 
> has occurred?
> >
> > Thanks, Eric
> >
> >
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