1KPZ: PEMV-1 P1-P2 Frameshifting Pseudoknot Regularized Average Structure

A hairpin-type messenger RNA pseudoknot from pea enation mosaic virus RNA1 (PEMV-1) regulates the efficiency of programmed -1 ribosomal frameshifting. The solution structure and 15N relaxation rates reveal that the PEMV-1 pseudoknot is a compact-folded structure composed almost entirely of RNA triple helix. A three nucleotide reverse turn in loop 1 positions a protonated cytidine, C(10), in the correct orientation to form an A((n-1)).C(+).G-C(n) major groove base quadruple, like that found in the beet western yellows virus pseudoknot and the hepatitis delta virus ribozyme, despite distinct structural contexts. A novel loop 2-loop 1 A.U Hoogsteen base-pair stacks on the C(10)(+).G(28) base-pair of the A(12).C(10)(+).G(28)-C(13) quadruple and forms a wedge between the pseudoknot stems stabilizing a bent and over-rotated global conformation. Substitution of key nucleotides that stabilize the unique conformation of the PEMV-1 pseudoknot greatly reduces ribosomal frameshifting efficacy.
PDB ID: 1KPZDownload
MMDB ID: 71237
PDB Deposition Date: 2002/1/3
Updated in MMDB: 2009/07
Experimental Method:
solution nmr
Biological Unit for 1KPZ: monomeric; determined by author
Molecular Components in 1KPZ
Label Count Molecule
Nucleotide(1 molecule)
P1-p2 Frameshifting Pseudoknot
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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