Highlighting RNA in a protein world

tRNA highlighted within a sea of proteins
29 May 2018

We may be called the Protein Data Bank in Europe, but the PDB archive contains more than just proteins. Many PDB entries also contain RNA, and we’ve just made finding them a lot easier.

RNA is vital to life, it carries both the genetic code and amino acids to the ribosome, where the RNA catalyses the synthesis of proteins. But it’s the ‘poor cousin’ to proteins in the PDB, lacking much of the standard naming and classification that proteins enjoy. This makes it difficult to find, for example, all the transfer RNAs.

Until now! Many RNA molecules are classified by Rfam, a database of non-coding RNA families based, like us, at the European Bioinformatics Institute (EMBL-EBI). We’ve worked together with our colleagues at Rfam to make use of their mappings of RNA molecules present in the PDB.

About half of the RNAs in the PDB are currently mapped to an Rfam family, but that figure rises to 94% for RNAs longer than 75 nucleotides and 99% for those above 500 nucleotides. You can now search using Rfam information (for instance, to find all the transfer RNAs) in PDBe’s search system. Rfam family names, clans and their accessions are supported.

Not only this, but Rfam sequence domains are shown on PDBe entry pages, just like they are for proteins classified by Pfam. There’s an image highlighting the Rfam domain within the molecule, and it can also be selected and highlighted in the sequence viewer which works interactively with LiteMol, so you can see where it is in 3D.

Screenshot of tRNA on PDBe entry page 

Highlighting an Rfam domain in the sequence of a tRNA (top) and (bottom) at the same time its location within a ribosome structure (PDB entry 4ujd).

Due to the collaboration between PDBe and Rfam, finding different RNA types at PDBe is much easier. Anton Petrov, Project Leader for RNA Resources at EMBL-EBI, said “Using Rfam annotations is a big step for improving access to RNA 3D structures at PDBe. Rfam computational models classify RNA structures into families and provide consistent and informative annotations across the entire database. Working on this project with PDBe also helped us improve Rfam 3D annotations by removing redundancy and improving coverage.”