1ESY

NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM

Summary for 1ESY

• Entry DOI: 10.2210/pdb1esy/pdb
• Related: 1BN0
• Descriptor: RNA (5'-R(P*GP*GP*CP*GP*AP*CP*UP*GP*GP*UP*GP*AP*GP*UP*AP*CP*GP*CP*C)-3') (1 entity in total)
• Functional Keywords: hiv-1, rna, splice-donor site, platform motif
• Total number of polymer chains: 1
• Total formula weight: 6148.71

Authors

Amarasinghe, G.K.,De Guzman, R.N.,Turner, R.B.,Summers, M.F. (deposition date: 2000-04-11, release date: 2000-05-31, Last modification date: 2024-05-01)

Primary citation

Amarasinghe, G.K.,De Guzman, R.N.,Turner, R.B.,Summers, M.F.
NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform.
J.Mol.Biol., 299:145-156, 2000

PubMed Abstract: 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.

PubMed: 10860728
DOI: 10.1006/jmbi.2000.3710

Experimental method

SOLUTION NMR