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One of my professors mentioned something about the e-site (the exit site for the t-RNA) on a eukaryotic ribosome. There was a student in the class who objected, saying that there is no e-site on eukaryotic ribosomes; it only exists on prokaryotic ribosomes. I've tried to find some reliable source to figure out who's right, but to date the only thing I've found is an obscure sentence in a wikipedia article, which doesn't look all that official.

Is there indeed an e-site on the eukaryotic ribosome?

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    $\begingroup$ ncbi.nlm.nih.gov/pmc/articles/PMC3331703/#s4title $\endgroup$ – theforestecologist Nov 9 '18 at 17:24
  • $\begingroup$ case.edu/med/coller/Coller%20C3MB%20Lecture%201.pdf $\endgroup$ – theforestecologist Nov 9 '18 at 17:29
  • $\begingroup$ @theforestecologist — citing a peer-reviewed publication is acceptable evidence because the references therein can be followed up. Citing somebody's lecture notes is not. $\endgroup$ – David Jul 4 at 20:18
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    $\begingroup$ Both are acceptable. Just like citing Wikipedia is acceptable here. However, I agree that a peer-reviewed publication is often an optimal resource. $\endgroup$ – theforestecologist Jul 5 at 0:43
  • $\begingroup$ Why not do the research yourself? Download a free copy of pymol and start looking at ribosomes from the pdb database... You might want to compare bacterial and eukaryotic ribosome structures. Try identifying the A,P and E sites. It will be a nice little project and you will learn a lot doing it $\endgroup$ – Jeppe Nielsen Jul 5 at 2:00
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Prelude: Thinking about protein synthesis

I remember the time when there were only two sites on the ribosome, and when it became clear there were more, I resented the need to make my lecture notes and my contribution to a venerable text book more complicated. So I am neither a devotee nor an expert on the exit site, but if asked to guess who was right (even if, or especially if, the student was supported by Campbell’s Biology as @CSharp informs us) I would put my money on the ‘professor’. Why? Because protein synthesis and the ribosome are so ancient that although there have been changes in eukaryotic proteins synthesis, something so fundamental as the sites for the fundamental process would not change.

Answer

Yes, Virginia, the eukaryotic ribosome does have an exit site.

The evidence

Although editions of the venerable text book no longer appear and my research no longer impinges on protein biosynthesis, I still collect papers on the subject with my bibliographic software. The latest relevant publication I have is by Khatter et al. from Nature in 2015, entitled Structure of the Human 80S Ribosome.

As not all list members have access to Nature, as a subscriber I have taken the liberty to reproduce a a section from the abstract (my emphasis) and a pertinent illustration:

Here we report the near-atomic structure of the human ribosome derived from high-resolution single-particle cryo-electron microscopy and atomic model building. The structure has an average resolution of 3.6A ̊, reaching 2.9A ̊ resolution in the most stable regions. It provides unprecedented insights into ribosomal RNA entities and amino acid side chains, notably of the transfer RNA binding sites and specific molecular interactions with the exit site tRNA.

Human ribosomal E-site

The cryo-EM map and atomic coordinates have been deposited in the EMDB and Protein Data Bank under accession codes EMD-2938 and 4ug0, respectively.

I admit I haven’t researched and rehearsed the evidence, but I think that would be another question.

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  • $\begingroup$ Here is an open access source for structural information regarding the eukaryotic ribosome, figure 3 in particular seems to contain the answer to the question being asked. ncbi.nlm.nih.gov/pmc/articles/PMC3331703 $\endgroup$ – Jeppe Nielsen Jul 5 at 2:15
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No. According to page 369 of the 9th edition of Biochemistry by Campbell:

"The structure of the eukaryotic ribosome is different in that there is no E site, only the A and P sites."

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    $\begingroup$ Welcome to SE Biology, Unfortunately Campell is a general biology text book, not a more specialist biochemistry or molecular biology text, which is where you are likely to find a better coverage of ribosomes. I do not have a copy of Campbell but I see from Amazon that it is now in its 11th edition, so perhaps this mistake (see my own answer) has been corrected now. $\endgroup$ – David Jul 4 at 20:31
  • $\begingroup$ Down voted due to low information content in the answer. You refer to a book which state the structure is different, but you do not go into much depth of how they are different. Also, how old is the book... $\endgroup$ – Jeppe Nielsen Jul 5 at 2:06
  • $\begingroup$ @CSharp Welcome to biology stack exchange! We appreciate your well-cited answer. I just wanted to ensure you that the downvotes you are getting on your answer appear to be due to the accuracy of your source and not the quality of your answer. Even downvoted answers like this are sometimes useful as they clarify a common misconception or point out inaccurate, commonly-used sources. Please don't be discouraged, and I invite you to check out our tour and welcome you to continue posting here. Thanks! $\endgroup$ – theforestecologist Jul 5 at 12:50
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    $\begingroup$ Further to the remark from @theforestecologist, although I think your answer incorrect I did not downvote you because you provided support for your conclusion. You were just unlucky to hit a mistake in a text book. One wonders whether that same mistake provoked the original controversy. $\endgroup$ – David Jul 5 at 13:47

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