Last modified on 30 March 2006.
Literature Reference:
Lee J.C., Gutell R.R., and Russell R. (2006)
The UAA/GAN Internal Loop Motif: A New RNA Structural Element That Forms a Cross-strand AAA Stack and Long-range Tertiary Interactions.
Journal of Molecular Biology 360:978-988.
Manuscript Tables and Figures:
| Table 1: The UAA/GAN Motifs and Their Tertiary Contacts Mediated by the Cross-strand AAA Stack |
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| Fig. 1: Locations of the UAA/GAN Motifs and Their Related Motifs |
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| Fig. 2: Schematic Representation of the UAA/GAN Motifs and Their Tertiary Interactions in the 23S rRNA |
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| Fig. 3: Stereoviews of the Structures and Tertiary Contacts of the UAA/GAN Motif |
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| Fig. 4: Helix Bending Caused by the UAA/GAN Motif and Their Close Relatives |
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| Fig. 5: A-minor Tertiary Interactions Mediated by the Cross-strand AAA Stack of the UAA/GAN Motif |
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Supplementary Tables and Figures:
| Supplementary Table 1: Sequence Variations for the UAA/GAA Motifs in 23S rRNA |
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| Supplementary Table 2: The UAA/GAN Motifs and Their Structural and Comparative Data |
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| Supplementary Fig. 1: Stereo Images for the Other Two UAA/GAN Motifs and Their Tertiary Interactions |
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| Supplementary Fig. 2: Pairwise Superpositions of the UAA/GAN and Other Motifs Forming a Cross-strand AAA Stack |
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| Supplementary Fig. 3: Tertiary Interactions Mediated by the Cross-strand AAA Stack of the UAA/GAN Motif |
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Additional Information: RasMol Scripts for Motif Structures and Tertiary Interactions
The UAA/GAN Motifs and Their Tertiary Interactions
Three-Dimensional Distribution of the UAA/GAN Motifs
| Distribution of the UAA/GAN Motifs in the H. marismortui 23S rRNA Crystal Structure |
RasMol Script |
| Distribution of the UAA/GAN Motifs in the B. stearothermophilus RNase P RNA Crystal Structure |
RasMol Script |
The UNA/GAN and GA/GAA Motifs and Their Tertiary Interactions (Two Related Motifs)
See manuscript, Figure 1, for additional information about these motifs.
| Location |
T16S |
H23S |
D23S |
E16S | E23S |
| T16S-635 (E16S-652) |
UAG/GAC |
-- |
-- |
UUG/GAC | -- |
| H23S-2242 (E23S-2197) |
-- |
UCA/GAC |
UAA/GAC |
-- | UAA/GAC |
| T16S-1414 |
GAA/GA |
-- |
-- |
-- | -- |
| H23S-564 |
-- |
GAA/GA |
-- |
-- | -- |
| E23S-1527 |
-- |
-- |
-- |
-- | GA/GAA |
Acronyms for crystal structures used and their PDB IDs:
- H23S: H. marismortui 23S rRNA (PDB 1FFK and 1JJ2)
- D23S: D. radiodurans 23S rRNA (PDB 1LNR)
- E23S: E. coli 23S rRNA (PDB 2AW4)
- T16S: T. thermophilus 16S rRNA (PDB 1FJF)
- E16S: E. coli 16S rRNA (PDB 2AVY)
- RNaseP: B. subtilis RNase P RNA (PDB 1NBS) and B. stearothermophilus RNase P RNA (PDB 2A64)
