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. The HTML viewer works well up to about 3000 nucleotides; after that it works better to download the PDF version and view it in a dedicated PDF viewer.
| 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
The Tetrahymena ribozyme features kissing hairpin pseudoknots.
Helices are labeled with a large font size, and basepairs are labeled with text around the outside of the circle.
Example 2
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, assigns standard labels to the chains,
and labels the helices in 5S, LSU, SSU, and tRNAs.
Outside the circle, basepair interactions are listed.
Example 3
Human large ribosomal subunit and 5.8S chain, drawn in grayscale. 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 4
The bacteriophage Phi-29 viral genome packaging motor assembly has five-fold symmetry.
This rendering using a safer palette for color blindness.
Example 5
This NMR structure shows 7 models of a DNA triple helix, with nested Watson-Crick basepairs
shown in blue and triple helix pairs with crossing green arcs.
There is variability in the pairing across the models.
Example 6
RNA G-quadruplex formed through interactions between one chain and its symmetry-generated counterpart.
Example 7
Structure 4V9O has four complete ribosomes in assemblies 1, 2, 3, 4.
Here we see assembly 4 followed by assembly 2.
Example 8
Plant mitochondrial large subunit ribosomal RNA, with helices numbered.
Example 9
Toxoplasma gondii mitochondrial ribosomal large subunit in 32 chains.
Note the interaction types which bind the chains to one another.
Helix numbering is not available for short matches to Rfam.
Compare to the plant mitochondrial large subunit above.
Example 10
Two assemblies of a DNA double helix with DG triphosphate ligand associated with a protein chain.
In one assembly DGT makes a Watson-Crick basepair, in the other just a stacking interaction.
The ligand chain appears in a natural location between DNA chains.
Example 11
Chain A interacts with a symmetry operated counterpart of Chain A.
Example 12
Rather than ordering alphabetically, chains are ordered to keep Watson-Crick paired chains
adjacent to one another.
Example 13
Viral capsid. Assembly 1 has 60 repetitions of the same unit using symmetry operators.
Assembly 3 has five units. Assembly 4 has six units.