The RNA 3D Motif Correspondence Server allows querying RNA 3D motifs or specific nucleotide sets in an RNA-containing PDB structure. It then identifies corresponding nucleotides in other structures of the same molecule type from the same species or different species. The results are presented in a table based on geometric similarity, with more similar instances grouped together. An interactive heatmap with a 3D viewer visually displays the geometric differences between the motif instances. The formation of separate clusters in the heatmap may indicate variable motif geometries linked to biological function or ligand binding. R3DMCS is pronounced "Red Max".
Example 1
Decoding loop across E. coli small subunit ribosomal RNA 3D structures at 3.0A resolution or better. This example illustrates the dynamic nature of the decoding loop.
Example 2
Internal loop from the small subunit ribosomal RNA helix 27, compared across species in the associated Rfam family RF00177 at resolution 4.0A or better, and including just one instance from each species. Most instances have the characteristic GUA base triple of the sarcin-ricin internal loop, but in four mitochondrial species, the G is replaced by C and the C is bulged out of the motif, not participating in the base triple.
Example 3
GNRA hairpin loop from Helix 34 of the large subunit ribosomal RNA, compared across different species in the associated Rfam family solved at resolution 4.0A or better, with up to 3 instances from each species. This example illustrates how some structures (in this case, the models of Triticum aestivum) model the top adenine base of the GNRA in syn while others model that base in anti. Other variability is also evident.
In addition to R3DMCS, several other APIs are available, where one can input unit ids or loop ids or chain ids and get back useful information. BGSU RNA APIs