PDBsum entry 1cx0

RNA binding protein/RNA

PDB id: 1cx0

Contents

Protein chain

95 a.a. *

DNA/RNA

Metals

_MG ×12

Waters ×64

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of a hepatitis delta virus ribozyme.

Authors

A.R.Ferré-D'Amaré, K.Zhou, J.A.Doudna.

Ref.

Nature, 1998, 395, 567-574. [DOI no: 10.1038/26912]

PubMed id

9783582

Abstract

The self-cleaving ribozyme of the hepatitis delta virus (HDV) is the only catalytic RNA known to be required for the viability of a human pathogen. We obtained crystals of a 72-nucleotide, self-cleaved form of the genomic HDV ribozyme that diffract X-rays to 2.3 A resolution by engineering the RNA to bind a small, basic protein without affecting ribozyme activity. The co-crystal structure shows that the compact catalytic core comprises five helical segments connected as an intricate nested double pseudoknot. The 5'-hydroxyl leaving group resulting from the self-scission reaction is buried deep within an active-site cleft produced by juxtaposition of the helices and five strand-crossovers, and is surrounded by biochemically important backbone and base functional groups in a manner reminiscent of protein enzymes.

Figure 4.
Figure 4 Structural components of the active site. a, Solvent-accessible surface of the ribozyme-U1A-RBD complex, orientated as in Fig. 3a, colour-coded by its curvature (green, convex; grey, concave^49). The atoms of the ribose ring of G1 are shown as red spheres; the 5'-hydroxyl group points away from the reader into the ribozyme. The trajectory proposed to be followed by nucleotides located 5' of the cleavage site in the precursor is indicated by the row of small red dots. b, The substrate-bearing nucleotide G1 forms a wobble pair with U37 which stacks on P1.1. The 5'-hydroxyl group (shown as a larger sphere) is within hydrogen-bonding distance of the Watson-Crick face of C75. Nucleotides are coloured as in Figs 2 and 3. Phosphorus atoms are coloured green. Oxygen and nitrogen atoms that participate in noteworthy hydrogen bonding (denoted by two-headed arrows) are coloured red and blue, respectively. c, Triple-strand junction between P3 and P1, orientated as in Fig. 3a. A hydrogen bond between the N1 group of A78 and the O2' group of G29 is obscured in this view.

Figure 5.
Figure 5 Structural features of the active site. a, The P3-L3 niche cradles the active site. The stereoview shows how the phosphate ribose backbone crosses over from the P3-L3 stack to P1.1 and back, passing through the unstacked nucleotide U23. The ribose of G1 and the bases of the stacked nucleotides from J4/2 are shown. b, The P1.1 helix and the pedestal. c, A A-weighted 2|F[o]| - |F[c]| map44,45, with data from 20 to 2.3 Å, contoured at 1 s.d., showing the nucleotides of J4/2 as seen from the major groove of P1. d, The trefoil turn (orientated roughly as in Fig. 3b) is the sharp twist in the RNA chain between G74 and A77. This is stabilized by a complex network of interactions between O2' groups and phosphate oxygens, a two-tiered ribose zipper, and base-backbone hydrogen bonds. Figures 3, 4b, c and 5a, b, d were prepared with RIBBONS50.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1998, 395, 567-574) copyright 1998.