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

Tue Dec 2 01:38:31 PST 2014

Dear Irina,
	I agree with the other replies that this is a key question for the EM community now.
	We recently had a similar "cas de conscience”, but with a crystal structure docking to an even much lower resolution map, where it is absolutely obvious that none of the side chains can be accurate (and maybe the polypeptide chain fold isn’t vaguely right in places!). We decided to deposit the pseudoatomic model in the pdb anyway, partly because it is what EMDB recommend, partly because our journal editor also said he felt it was appropriate but also partly because we felt that if we didn’t nobody could independently reassess/test/use our work in the future. Now, in theory, all those accessing such files should be able to figure out for themselves how accurate the models are but, in reality, many I feared would be fooled into taking their visual accuracy for granted. So, we decided to put a “resolution health warning” as a note in the deposition, which I requested would be available upfront to the downloaders. And, of course, we also discussed the crudeness of the resolution in the paper. 
	Regarding the rapidly increasing numbers of 4-5 Å resolution cryoEM maps, I think we should also caution reviewers and users about relying on the rotamer libraries and MD (rather than additional ED map refinement, where possible, which should be done by authors) to improve the pseudoatmoic models. That is mixing modelling with experimental data in ways that, as far as I know, are not properly experimentally investigated/validated yet (but evidently need to be in future), and where there is therefore again serious concern about overinterpretation. So, if we chose do it, it should also be explicit in the deposition and paper.
	Best,
	Ariel.

Ariel J. Blocker, PhD, FSB
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On 2 Dec 2014, at 09:03, Petr Leiman <petr.leiman at epfl.ch> wrote:

> 
> 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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