RNA conformational classes

Abstract

RNA exhibits a large diversity of conformations. Three thousand nucleotides of 23S and 5S ribosomal RNA from a structure of the large ribosomal subunit were analyzed in order to classify their conformations. Fourier averaging of the six 3D distributions of torsion angles and analyses of the resulting pseudo electron maps, followed by clustering of the preferred combinations of torsion angles were performed on this dataset. Eighteen non-A-type conformations and 14 A-RNA related conformations were discovered and their torsion angles were determined; their Cartesian coordinates are available.

Figure 1

A chemical diagram of a dinucleotide fragment shows definitions of the backbone torsions.

Figure 2

Histograms for the six backbone torsion angles α, β, γ, δ, ε and ζ and the torsion χ at the glycosidic bond in 23S and 5S rRNA of the crystal structure of the 50S ribosomal subunit (NDB code RR0033, PDB code 1JJ2) (1,9).

Figure 3

Scattergrams (ζ_i, α_i+1), (ζ_i, β_i+1), (ζ_i, ε_i), (α_i, γ_i), (ζ_i, χ_i) and (δ_i, χ_i) of 23S and 5S rRNA torsion angles from the crystal structure of the 50S ribosomal subunit (NDB code RR0033, PDB code 1JJ2) (1,9). Only 830 data points are shown; 2011 data points with torsion angle values ζ_i and α_i+1 at the phosphodiester link labeled as A-RNA with values of ζ_i ≈ 290° and α_i+1 ≈ 300° were excluded. See text for further details.

Figure 4

Two representations of a 3D distribution. (a) The distribution of torsion angles (ζ_i, α_i+1, δ_i) from rRNA of the 50S ribosome structure (NDB code RR0033, PDB code 1JJ2) (1,9). The 830 individual conformations (data points) are shown as blue crosses. (b) Fourier transform of point distribution (a) is rendered as pseudo electron density isocurves in light blue for ∼5% of the maximum density and red for 85% of the maximum density. In both (a) and (b), torsion ζ_i is approximately horizontal, α_i+1 is vertical and δ_i is perpendicular to the plane of the paper. Peak positions AA, B, C, D1, D2 etc. refer to sites of preferred values of torsions ζ_i, α_i+1, δ_i and were used to cluster residues of similar conformations. Both figures are in stereo.

Figure 5

Stereo views of three selected conformational RNA families identified in the 23S and 5S rRNA of the crystal structure of the 50S ribosomal subunit (NDB code RR0033, PDB code 1JJ2) (1,9): (a) conformation 1 with Z-DNA-like backbone but both bases in the anti orientation; (b) conformation 2 which is seen in the tetraloops with sequences RNRN; (c) conformation 7 with parallel bases as in the adenine platform. For further description of the conformations see Table 3 and text. Overlaps of individual dinucleotides are shown by thin lines. The representative averaged conformation is shown as ball-and-stick model using the chemical convention for coloring. The canonical A-RNA (pale green) is superimposed on the average conformation.

Figure 6

Gallery of the 19 RNA conformational families (conformations 1–19) in their averaged geometries and the canonical A-RNA (conformation 20). Dinucleotides were drawn with the 5′-end on top. All have sequence 5′-AU-3′ and are numbered as in Table 3 and the text.