R3DCID uses RNA and DNA 3D structure information (R3D) to produce Circular Interaction Diagrams (CID), which show basepair and other interactions within RNA and DNA 3D structures. R3DCID is pronounced like /red sid/. One or more models, assemblies, or chains can be shown. Users can customize the diagram using the interface below. For further guidance, see the examples or click on the "Help" button above. Clicking Submit will generate a one-page diagram in PDF format. Note: a PDF viewer will generally allow you to zoom in more on a diagram than a browser will.
| Show | Dim | Hide | Interaction |
|---|---|---|---|
| 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 | |||
| sugar-ribose interactions | |||
| oxygen stacking 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.
R3DCID automatically puts ribosomal chains in a standard order, and assigns standard labels to the helices 5S, LSU, SSU, and tRNAs.
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.
For a cleaner diagram, stacking and near interactions are not shown, and base-backbone interactions are dimmed.
Example 3
The Tetrahymena ribozyme features kissing hairpin pseudoknots.
Here, arcs are drawn with a safer palette for color blindness, helices are labeled with a large font size, and all interactions are labeled with text around the outside of the circle.
Example 4
The bacteriophage Phi-29 viral genome packaging motor assembly has five-fold symmetry,
which is clear in this grayscale rendering of the circular interaction diagram.
Example 5
NMR structure with 20 models of a two-chain duplex, with varying numbers of annotated Watson-Crick
basepairs. All nucleotides in this structure have a modified backbone with non-standard chirality.
Example 6
RNA-DNA duplex with two assemblies and some inter-assembly interactions.
Basepair, stacking, and base-phosphate interactions are annotated.
Example 7
G-quadruplex formed through interactions between one chain and its symmetry-generated counterpart.
Example 8
Structure 4V9O has four complete ribosomes in assemblies 1, 2, 3, 4.
Here we see assembly 4 followed by assembly 1.