DSSR is used for the analysis of CRISPR PbuCas13b-crRNA

Recently I read with great interest the article High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage by Slaymaker et al., published in Cell Reports (2019, 26, 3741–3751). This 1.65-Å structure (PDB id: 6dtd) “provides a mechanistic model for Cas13b target RNA recognition and identifies features responsible for target and cleavage specificity.”

I am pleased to see that DSSR is listed in the “KEY RESOURCES TABLE” under the category “Software and Algorithms”, and mentioned in the “Structure Analysis” section:

RNA structure was analyzed using DSSR (Lu et al., 2015). Protein conservation mapping to the structure was done using the Consurf server (Ashkenazy et al., 2016). Protein secondary structure was analyzed using the PDBSUM webserver (de Beer et al., 2014) (Figure S1E). APBS as part of the PyMOL visualization program was used to calculate electrostatics (Jurrus et al., 2018). Structure validation statistics were generated with MolProbity (Chen et al., 2010)

In the main text, the authors cited DSSR for the detection of a base multiplet. Running DSSR on PDB entry 6dtd, I found two base triplets, as shown below:

In the figure above, each of the two adenines is interacting with a G–C pair in the minor-groove edge (m) of the pair: A30 (left) is using its Watson-Crick edge (W), whilst A23 (right) is employing its major-groove edge (M). Thus they do not belong to the canonical A-minor motifs (types I or II) where the minor-groove edge of A interacts with the minor-groove edge of a WC pair. In DSSR, they are classified as type=X, a general category of noncanonical A-minor motifs.





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