1PJY

Solution structure of the HIV-1 frameshift inducing stem-loop RNA

Summary for 1PJY

• Entry DOI: 10.2210/pdb1pjy/pdb
• NMR Information: BMRB: 5834
• Descriptor: HIV-1 frameshift inducing stem-loop (1 entity in total)
• Functional Keywords: frameshift, hiv, tetraloop, rna structure, rna
• Total number of polymer chains: 1
• Total formula weight: 7071.30

Authors

Staple, D.W.,Butcher, S.E. (deposition date: 2003-06-04, release date: 2003-08-05, Last modification date: 2024-05-22)

Primary citation

Staple, D.W.,Butcher, S.E.
Solution structure of the HIV-1 frameshift inducing stem-loop RNA.
Nucleic Acids Res., 31:4326-4331, 2003

PubMed Abstract: The translation of reverse transcriptase and other essential viral proteins from the HIV-1 Pol mRNA requires a programmed -1 ribosomal frameshift. This frameshift is induced by two highly conserved elements within the HIV-1 mRNA: a slippery sequence comprised of a UUUUUUA heptamer, and a downstream stem-loop structure. We have determined the structure of the HIV-1 frameshift inducing RNA stem-loop, using multidimensional heteronuclear nuclear magnetic resonance (NMR) methods. The 22 nucleotide RNA solution structure [root mean squared deviation (r.m.s.d.) = 1.2 A] was determined from 475 nuclear Overhauser effect (NOE)-derived distance restrains, 20 residual dipolar couplings and direct detection of hydrogen bonds via scalar couplings. We find that the frameshift inducing stem-loop is an A-form helix capped by a structured ACAA tetraloop. The ACAA tetraloop is stabilized by an equilateral 5' and 3' stacking pattern, a sheared A-A pair and a cross-strand hydrogen bond. Unexpectedly, the ACAA tetraloop structure is nearly identical to a known tetraloop fold, previously identified in the RNase III recognition site from Saccharomyces cerevisiae.

PubMed: 12888491
DOI: 10.1093/nar/gkg654

Experimental method

SOLUTION NMR