[3dem] pdb for near-atomic resolution EM maps

[Petr Leiman]

On 12/02/2014 08:43 AM, Irina Gutsche wrote:
>
> Dear all,
>
> I would like to deposit a near-atomic resolution map (4.3A) and the 
> corresponding atomic model to the respective databases. Given recent 
> discussions about overinterpretation of the data I am wondering what 
> would be the best way to proceed.
> Indeed, some bulky side chains are clearly visible and could be placed 
> with confidence, in particular in certain regions of the map 
> (according to ResMap local resolution ranges from 3.5A to above 6A), 
> but most of them not. And even the criteria of "visibility" and 
> "confidence" are subjective. The protein complex is of big 
> pharmaceutical interest and I suppose that if the complete pdb with 
> all the side chains is deposited, it may be downloaded and used for 
> example for drug design, as a kind of "absolute truth", which might be 
> dangerous. However, deposit only the c-alpha is probably too 
> restrictive. Another option would be to deposit only the side chains 
> we are "sure about", but again, it's subjective, and anyway we can 
> only be "sure" at the given resoluition. So what would be the most 
> honest and unbiased way to share these results with the scientific 
> community, in particular with biologists who are not necessarily aware 
> of the overinterpretation/overfitting/validation/etc issues in our 
> field but who use our results to design their experiments?

This kind of topic is discussed at crystallographic BBs at length about 
once a year for as long as those boards exit. There, however, people 
discuss what to do with side chains for which there is no density. Build 
them or truncate at C-alpha or C-beta or make them zero occupancy or let 
the refinement take care of the problem (it will elevate the B factor to 
hundred(s) of A^2). These discussions are endless for the exact same 
reasons that Irina has brought up.

In the case of 3.5-6 A resolution structure, the experimental error of 
atomic positions is so high that you build your side chains based on the 
rotamer database, but not on the density. There is also an uncertainty 
(e.g. error) associated with placing the main chain, but let's forget 
about this for a second. My point: for these "almost atomic 
interpretation" datasets, the information contained in the main chain 
that is placed into the density to the best of our ability is all that 
is required to recreate the complete atomic model. For simple 
interpretations and ribbon diagrams, the main chain information is 
sufficient. But people who want to design drugs will have to look into 
the model a little more. They will have to rebuild all the side chains 
(they will rely on the rotamer library for doing so - exactly what we do 
now) and perform MD and/or additional refinement. And of course, the 
main chain model should contain all the side chains for which there is 
good experimental density.

Best wishes,

Petr

>
> Thank you very much for your all ideas and suggestions,
>
> Best regards,
>
> Irina Gutsche
> CNRS, Grenoble,
> France
>
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-- 
Petr Leiman
Laboratory of Structural Biology and Biophysics
http://lbbs.epfl.ch

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