Tuesday, July 3, 2012

Argonaute I and Argonaute II

Structure of Yeast Argonaute with Guide RNA
Kotaro Nakanishi, David E. Weinberg, David P. Bartel, Dinshaw J. Patel
Nature (2012), 486, 368-373

This week brings exciting news for the RNA-world.
The group of Dinshaw Patel has published a new Argonaute structure which includes its guide RNA.
The structure can be found at the Protein Data Bank under the 4f1n identifier and it was solved at 3.2 Angstrom resolution.
Some weeks ago I posted here the news of Schirle and Macrae's new 2.3 Angstrom structure of Argonaute II.
So, now both Argonaute I (in the left side of the movie) and Argonaute II (in the right side of the movie) with their corresponding guide RNA's can be compared side by side, and they are quite similar in shape.
If one does a partial alignment of the structures using the default alignment parameters of pymol, one gets that the two structures align with an RMSD of 3.8 Angstroms.
Again, a movie is quite useful and we have made a very short one as you can see below: