Hello
I'm trying to develop a protein folding prediction software. I was studying this paper "Structures of the human and Drosophila 80S ribosome" about the PDB 4V6X. I'm wondering if someone could help me find the exit tunnel for the protein on this structure (4V6X). If I can have just the sequence number of one atom on the exit surface would help me a lot.
The reason for that is that I'm having problems having the a-helix folding to the right direction and I'm would like to build a exit tunnel wall based on this PDB file to use as a start point for the born protein.
thanks a lot
Article Structures of the human and Drosophila 80S ribosome
I would not recommend you to use this structure for computation. The resolution is reported at 5 A so you would not know the side-chain position. If you want to use eukaryotic ribosome, you can try the original Tetrahymena thermophilia (resolution 3.5 A, http://www.mol.biol.ethz.ch/groups/ban_group/Ribosome ) , or yeast ribosome (resolution 2.8 A http://dx.doi.org/10.1038/nature13737 ).
But for easy orientation, use the T.thermophilia python session, you can find the tunnel by proteins RPL4, RPL17 and RPL23A. The tunnel exit (is marked by proteins RPL23A, RPL35, and RPL37.
Hope this helps.
@Jiri. Thanks so much for the links and for advice the exit tunnel place. That T.thermophilia python session clarified a lot. I didnt know that page. It really helped a lot.
@Jean. First, I would like to thanks for your paper on 4v6x. I have been over that structure for many days and was very interesting. I can just imagine how complex was to build it. Even to open is already a big deal for pymol. Also thanks for advising about the 4ug0.
I would like to share the result pdb and pymol file with the tunnel in case in the future somebody else came to this question looking for the same thing. I hope I got it right -).
https://docs.google.com/document/d/1eki9SMbXtc0Poi3J5lrlRyNv09Y_8NXDcSSEQaQ_3jM/edit?usp=sharing
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