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Background :

Hi! I am running a small experiment dealing with structural heterogeneity of the ribosome, actually of ribosomes across all domains of life. It's entirely computational: I get cryoEM samples(below) from PDB, parse the crystallographic profiles and see if I can enclose on physical clusters of proteins that persist across domains of life (i.e. uL4 reliably neighbors uL22 according to this ontology) and things like that. So far I've been working with the following dataset of eukaryotic/eubacterial/archeal macromolecules and am feeling pretty shackled by it at this point.


Question :

I would be very happy to augment this dataset with any number of "similar" ribosomes to put through the algorithm, but I don't know much about exemplar species to draw from and decided to ask here if somebody would recommend some more or less well-studied species(or straight-up PDB IDs) that would make a good addition. If you could point a boy to where I can "just get more" that'd be even more awesome. I'm not a biologist by training so you probably know of some obvious resource I don't.

I have no other constraints on what the targets are. Thank you so much and stay safe!

enter image description here I realize that most of these listed here are like the go-to organisms in biological research.

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  • $\begingroup$ If you have searched PDB (and that looks the case) you have what there is. I trust that you realize that a protein designated L4 in E. coli bears no relationship to the one designated L4 in eukaryotes. As far as I am aware there are very few similarities in structure between eukaryotic and prokaryotic ribosomal proteins, and in any case the nomenclature was in no way structural or functional, but based primarily on position on two-dimensonal electrophoresis. I am less familiar with the nomenclature of archaea ribosomal proteins, but these show differences from eukaryotes and eubacteria. $\endgroup$ – David Apr 4 '20 at 8:12
  • $\begingroup$ Thanks for the reply, @David. I should have included that, maybe, but didn't to keep it concise: I'm using the nomenclature system proposed by [Ban et al.] (bangroup.ethz.ch/research/…) which aspires to standardize on function and enables us to do actually run this study. That's the system in which I'm referring to uL22 and uL4 and all others. I figured out pretty quickly that chain ids on PDB have no particular rhyme or reason to them. $\endgroup$ – rtviii Apr 4 '20 at 15:06
  • $\begingroup$ @David when you are saying that PDB is all that there is, do you have any species in mind that I can search on there to get the ribosome of or is it whatever? My problem with the latter is most of the structures i see on there seem to be results of experimental depositions in which a ribosome just figures like Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1), but is not the main model. I wouldn't want to dilute my sample with anything but ribosomal structures. $\endgroup$ – rtviii Apr 4 '20 at 15:20
  • $\begingroup$ OK. Just thought I’d check. One way you might find ribosome structures in PDB is to search for a particular protein by number. It will also bring up that protein alone, of course. I wouldn’t have thought there was much interest in other species now, given the cost and effort involved, and the low publishability. There would have to be something special or different about the ribosomes. A recent review is the other approach, which I imagine you have tried. $\endgroup$ – David Apr 4 '20 at 15:56
  • $\begingroup$ @David, now we are talking. I can definitely relate to the point about the effort. It's been a pretty excruciating bead-stringing exercise wrt data-cleaning even before anything could begin to run. What do you mean by the recent review, though? I don't think i have! $\endgroup$ – rtviii Apr 4 '20 at 17:05

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