RNABase: an annotated database of RNA structures

Abstract

RNABase is a unified database of all three-dimensional structures containing RNA deposited in either the Protein Data Bank (PDB) or Nucleic Acid Data Base (NDB). For each structure, RNABase contains a brief summary as well as annotation of conformational parameters, identification of possible model errors, Ramachandran-style conformational maps and classification of ribonucleotides into conformers. These same analyses can also be performed on structures submitted by users. To facilitate access, structures are automatically placed into a variety of functional and structural categories, including: ribozymes, pseudoknots, etc. RNABase can be freely accessed on the web at http://www.rnabase.org. We are committed to maintaining this database indefinitely.

Figure 1

The cumulative number of publicly available RNA containing structures determined by X-ray crystallography (red), NMR spectroscopy (purple) and all techniques combined (blue) have been steadily increasing since the first RNA containing structure was released in 1978. There has been a substantial acceleration in RNA structure determination since the mid-1990s.

Figure 2

The average number of Ramachandran conformational map outliers per residue has shown no consistent trends over time for all structures (blue) or for the subsets determined by X-ray crystallography (red) and NMR spectroscopy (purple).

Figure 3

The average number of Ramachandran conformational map outliers per residue in structures solved by X-ray crystallography decreases with improving resolution (red). The average rate of outliers per residue for NMR structures (purple) is slightly worse than the overall average and is comparable to the rate for structures determined to ∼4 Å resolution. The data for X-ray structures are calculated as averages over 0.5 Å windows.