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Questions and answers => RNA structures (DSSR) => DSSR-NAR paper => Topic started by: xiangjun on July 07, 2015, 01:56:51 pm

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Title: Supplementary Figure 5 -- characterizing junction loops in twister ribozyme
Post by: xiangjun on July 07, 2015, 01:56:51 pm
(http://x3dna.bio.columbia.edu/dssr-nar/supp-fig5-twister-4rge/twister-junction-ribbons.png)
Quote
Figure S5: Ribbon representations of the junction loop in the env22 twister ribozyme (PDB id: 4rge). The ribbons are defined in terms of the C1′ and P atoms of the nucleotides that make up the junction loop. Inclusion of pseudoknots in the analysis of the structure reveals a [4,2,2,0,1,3,0,0,1,1] ten-way junction and a ribbon that follows a super-coiled pathway, with a linking number of three (blue, top row). Upon pseudoknot removal, only a [2,1,3] three-way junction and a ribbon with a simple relaxed circular configuration remain (green, bottom row). The overlap of the two junction loops in the middle row clearly shows that the over-simplified three-way junction spans only a small portion of the ten-way loop. The ribbons are shown in three projections: down the x-axis (left column), the y-axis (middle column), and the z-axis (right column). The images were kindly generated by Dr. Nicolas Clauvelin using the approach described in ref. 49.


Note:

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.