1kaj
From Proteopedia
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CONFORMATION OF AN RNA PSEUDOKNOT FROM MOUSE MAMMARY TUMOR VIRUS, NMR, 1 STRUCTURE
Overview
The solution conformation of an RNA pseudoknot, which is a mutant of the, pseudoknot required for ribosomal frameshifting in mouse mammary tumor, virus, has been determined by NMR. The 32-nucleotide RNA pseudoknot does, not promote efficient frameshifting, although its sequence is very similar, to the efficient frameshifting pseudoknot whose structure was recently, determined by our group. 13C-labeling of the RNA and 13C-edited NMR, techniques were used to facilitate spectral assignment. The, three-dimensional structure of the RNA pseudoknot was determined by, restrained molecular dynamics based on NMR-derived interproton distances, and torsion angle constraints. The conformation is very different from, that previously determined for the efficient-frameshifting pseudoknot. Two, unpaired nucleotides are stacked between stem 1 and stem 2, in contrast to, the one unpaired nucleotide at the same junction region as found, previously. The two stems of the pseudoknot are not coaxial, they are, twisted and bent relative to each other. Loop 2 does not cross the shallow, minor groove of stem 1, in contrast to the pseudoknots with one or no, intervening nucleotides between the stems. The fact that a specific, conformation is required for efficient frameshifting implies a specific, interaction of the pseudoknot with the ribosome.
About this Structure
1KAJ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Conformation of a non-frameshifting RNA pseudoknot from mouse mammary tumor virus., Kang H, Hines JV, Tinoco I Jr, J Mol Biol. 1996 May 31;259(1):135-47. PMID:8648641
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