1esy
From Proteopedia
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NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM
Overview
The genome of the human immunodeficiency virus type-1 (HIV-1) contains a, stretch of approximately 120 nucleotides known as the psi-site that is, essential for RNA packaging during virus assembly. These nucleotides have, been proposed to form four stem-loops (SL1-SL4) that have both independent, and overlapping functions. Stem-loop SL2 is important for efficient, recognition and packaging of the full-length, unspliced viral genome, and, also contains the major splice-donor site (SD) for mRNA splicing. We have, determined the structure of the 19-residue SL2 oligoribonucleotide by, heteronuclear NMR methods. The structure is generally consistent with the, most recent of two earlier secondary structure predictions, with residues, G1-G2-C3-G4 and C6-U7 forming standard Watson Crick base-pairs with, self-complementary residues C16-G17-C18-C19 and A12-G13, respectively., However, residue A15, which is located near the center of the stem, does, not form a predicted bulge, and residues A5 and U14 do not form an, expected Watson-Crick base-pair. Instead, these residues form a novel, A5-U14-A15 base-triple that appears to be stabilized by hydrogen bonds, from A15-H61 and -H62 to A5-N1 and U14-O2, respectively; from A5-H61 to, U14-O2, and from C16-H42 to U14-O2'. A kink in the backbone allows the, aromatic rings of the sequential U14-A15 residues to be approximately, co-planar, adopting a stable "platform motif" that is structurally similar, to the A-A (adenosine) platforms observed in the P4-P6 ribozyme domain of, the Tetrahymena group I intron. Platform motifs generally function in RNA, by mediating long-range interactions, and it is therefore possible that, the A-U-A base-triple platform mediates long-range interactions that, either stabilize the psi-RNA or facilitate splicing and/or packaging., Residue G8 of the G8-G9-U10-G11 tetraloop is stacked above the U7-A12, base-pair, and the remaining tetraloop residues are disordered and, available for potential interactions with either other RNA or protein, components.
About this Structure
1ESY is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform., Amarasinghe GK, De Guzman RN, Turner RB, Summers MF, J Mol Biol. 2000 May 26;299(1):145-56. PMID:10860728
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