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. 2005 Jun;3(6):e213.
doi: 10.1371/journal.pbio.0030213. Epub 2005 Jun 14.

Pseudoknots: RNA structures with diverse functions

David W Staple  1 , Samuel E Butcher
Affiliations

Pseudoknots: RNA structures with diverse functions

David W Staple et al. PLoS Biol. 2005 Jun.

Abstract

Just as proteins form distinct structural motifs, certain structures are commonly adopted by RNA molecules. Amongst the most prevalent is the RNA pseudoknot.

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Figures

Figure 1
Figure 1. RNA Pseudoknot Architecture
(A) Linear arrangement of base-pairing elements within an H-type RNA pseudoknot. Base pairing is indicated with dashed lines. (B) Formation of initial hairpin within pseudoknot sequence. Base pairings from loop to bases outside the hairpin are indicated with dashed lines. (C) Classic H-type pseudoknot fold. (D) Three-stemmed RNA pseudoknot fold from SARS-CoV.
Figure 2
Figure 2. Sequences and Structures of RNA Pseudoknots
Stems and loops are numbered sequentially, unless otherwise noted. Structure coordinates were obtained from the Protein Data Bank (http://www.rcsb.org), and structural representations were produced using MOLMOL software. (A) HDV (1SJ3). Numbering of stems reflects standard nomenclature for HDV. The U1A RNA binding domain is colored gray and is not included in the three-dimensional structure. (B) Diels-Alder ribozyme (DA-R) (1YLS). (C) Human telomerase (hTR) (1YMO). (D) MMTV (1RNK). (E) Pea enation mosaic virus RNA1 (PEMV-1) (1KPZ). (F) Simian retrovirus 1 (SRV-1) (1E95).
See this image and copyright information in PMC

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