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. 2023 Jul 3;51(15):8255–8269. doi: 10.1093/nar/gkad553

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© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — Fragments with strictly conserved sequence of porcine (A) and rabbit (B) expansion segments (ES7a) in 28S rRNA with corresponding cryo-EM reconstructions at 3.4Å and 3.0Å resolution, respectively. Black model on panel (A) and grey on panel (B) represent deposited coordinates whereas porcine structure with sequence re-assigned using doubleHelix is depicted in red. Aligned sequences and secondary structures of the rabbit and porcine models are presented on panel (C). Although the register shift in deposited porcine structure preserves most of the base-pairs (green and blue boxes), several of them are visible as clear density-fit outliers (bases in red rectangles and labelled on panel A). There are also multiple secondary structure violations (shown in orange). Secondary structure presented on panel (C) was identified from the corrected model using ClaRNA. The figure was prepared using ChimeraX (52) and R-chie webserver (53).