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Major centers of motion in the large ribosomal RNAs.

Paci M, Fox GE - Nucleic Acids Res. (2015)

Bottom Line: Of the 21 pivots found, six are observed in the large subunit rRNA and 15 in the small subunit rRNA.The pivoting positions are typically associated with structurally weak motifs such as non-canonical, primarily U-G pairs, bulge loops and three-way junctions.These helices are envisioned to form a network.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biochemistry, University of Houston, 4800 Cullen Blvd. Houston, TX 77204-5001, USA.

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Secondary structure of T. thermophilus 16S rRNA highlighting the details of each pivoting element. The stem sequences that were superimposed are highlighted in black. Pivoting elements are shown in red and final stems are shown in green. Helices 29 and 34 are considered to be final helices by our definition of a pivot, even though they are internal. They are therefore color coded in green as are the external final helices. The figure thus highlights the connectivity between pivoting helices 28, 32 and the remainder of the SSU head domain.
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Figure 3: Secondary structure of T. thermophilus 16S rRNA highlighting the details of each pivoting element. The stem sequences that were superimposed are highlighted in black. Pivoting elements are shown in red and final stems are shown in green. Helices 29 and 34 are considered to be final helices by our definition of a pivot, even though they are internal. They are therefore color coded in green as are the external final helices. The figure thus highlights the connectivity between pivoting helices 28, 32 and the remainder of the SSU head domain.

Mentions: Initially, elongation factor G (EF-G) unbound ribosomes (26) from T. thermophilus were compared with EF-G bound structures in various states (12,28). These comparisons revealed 21 hinge-like regions in the 16S and 23S rRNAs, which likely act to accommodate the forward translation process. Of these, many were not previously explicitly described. The newly discovered pivot points are found primarily in the small subunit in helices h6-the spur, h8, h21, h26 as well as in the majority of the helices in the 3′ major domain (h31, h32, h33, h36, h37, h39, h40, h41, h42 and h43). The location of these pivots is shown in the context of the T. thermophilus 16S rRNA secondary structure (Figure 2). Pivots found in the 23S rRNA are in helices H34, H38, H42, H69, H76 and H84. Their location is shown on Supplementary Figure S1 utilizing the secondary structure model that was recently derived from tertiary structure (32,33). More detailed displays that also highlight the stems that were superimposed and final stems are shown in Figures 3 and 4. Subsequently, 12 additional comparisons were undertaken for E. coli (7,29) and S. cerevisiae (30) ribosomes. Equivalent pivots were typically found, thereby demonstrating their conservation. It should be noted, however, that intersubunit rotation may not always be correlated with head rotation or L1 stalk movement.


Major centers of motion in the large ribosomal RNAs.

Paci M, Fox GE - Nucleic Acids Res. (2015)

Secondary structure of T. thermophilus 16S rRNA highlighting the details of each pivoting element. The stem sequences that were superimposed are highlighted in black. Pivoting elements are shown in red and final stems are shown in green. Helices 29 and 34 are considered to be final helices by our definition of a pivot, even though they are internal. They are therefore color coded in green as are the external final helices. The figure thus highlights the connectivity between pivoting helices 28, 32 and the remainder of the SSU head domain.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482067&req=5

Figure 3: Secondary structure of T. thermophilus 16S rRNA highlighting the details of each pivoting element. The stem sequences that were superimposed are highlighted in black. Pivoting elements are shown in red and final stems are shown in green. Helices 29 and 34 are considered to be final helices by our definition of a pivot, even though they are internal. They are therefore color coded in green as are the external final helices. The figure thus highlights the connectivity between pivoting helices 28, 32 and the remainder of the SSU head domain.
Mentions: Initially, elongation factor G (EF-G) unbound ribosomes (26) from T. thermophilus were compared with EF-G bound structures in various states (12,28). These comparisons revealed 21 hinge-like regions in the 16S and 23S rRNAs, which likely act to accommodate the forward translation process. Of these, many were not previously explicitly described. The newly discovered pivot points are found primarily in the small subunit in helices h6-the spur, h8, h21, h26 as well as in the majority of the helices in the 3′ major domain (h31, h32, h33, h36, h37, h39, h40, h41, h42 and h43). The location of these pivots is shown in the context of the T. thermophilus 16S rRNA secondary structure (Figure 2). Pivots found in the 23S rRNA are in helices H34, H38, H42, H69, H76 and H84. Their location is shown on Supplementary Figure S1 utilizing the secondary structure model that was recently derived from tertiary structure (32,33). More detailed displays that also highlight the stems that were superimposed and final stems are shown in Figures 3 and 4. Subsequently, 12 additional comparisons were undertaken for E. coli (7,29) and S. cerevisiae (30) ribosomes. Equivalent pivots were typically found, thereby demonstrating their conservation. It should be noted, however, that intersubunit rotation may not always be correlated with head rotation or L1 stalk movement.

Bottom Line: Of the 21 pivots found, six are observed in the large subunit rRNA and 15 in the small subunit rRNA.The pivoting positions are typically associated with structurally weak motifs such as non-canonical, primarily U-G pairs, bulge loops and three-way junctions.These helices are envisioned to form a network.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biochemistry, University of Houston, 4800 Cullen Blvd. Houston, TX 77204-5001, USA.

Show MeSH
Related in: MedlinePlus