The Circular Diagram Server offers 2D diagrams illustrating interactions within RNA structures. It presents a wider range of information compared to their 3D counterparts, allowing for easier visualization of complex data. This feature facilitates the transformation of intricate details from 3D RNA structures into a comprehensible 2D format, maintaining essential information while simplifying visualization. Users can specify key details about the RNA structure, and upon submission, receive a corresponding diagram in PDF format. For further guidance, click on the "Help" button above.
| Show | Dim | Hide | Interaction |
|---|---|---|---|
| between chains | |||
| within chains | |||
| nested Watson-Crick basepairs | |||
| non-nested Watson-Crick basepairs | |||
| nested non-Watson-Crick basepairs | |||
| non-nested non-Watson-Crick basepairs | |||
| stacking interactions | |||
| base-phosphate interactions | |||
| base-ribose interactions | |||
| near interactions |
Example 1
Complete Escherichia coli ribosome showing the 5S chain, large subunit, small subunit,
and two tRNAs bound to the LSU and SSU and interacting with mRNA.
Example 2
Human large ribosomal subunit and 5.8S chain. These chains have more than 5000 nucleotides,
but large segments of chain L5 do not have 3D coordinates in the solved structure, and so are represented with base and sequence position only.
Stacking and near interactions are not shown, and base-backbone interactions are dimmed.
Example 3
This eukaryotic ribozyme from Tetrahymena thermophila contains three pseudoknots, two of which are kissing hairpin interactions.
The arcs are colored using the Wong color palette, designed to enhance color discrimination..
Example 4
This presents the 8OM4 molecule, recognized as the small subunit ribosomal RNA (SSU rRNA),
originating from mitochondria, specifically from Saccharomyces cerevisiae, commonly known as baker's yeast. The diagram employs grayscale
coloring and highlights only the nested cWW interactions while reducing the prominence of long-range cWW interactions.
Example 5
Here we present the crystal structure of chlorolissoclimide bound to the yeast 80S ribosome,
with emphasis on the interactions between chains 5TBW|1|1 and 5TBW|1|4.
This structure offers significant insights into the binding mechanism of chlorolissoclimide, a potential antifungal agent, to the ribosome.
Example 6
The structure of the mitochondrial ribosome from Tetrahymena thermophila
is classified under ribosome. Here we
focus on chains 6Z1P|1|Ab and 6Z1P|1|Aa. By dimming all inter-chain interactions,
we can concentrate on intra-chain interactions while still maintaining an understanding
of the inter-chain dynamics.