1G70

COMPLEX OF HIV-1 RRE-IIB RNA WITH RSG-1.2 PEPTIDE

Summary for 1G70

• Entry DOI: 10.2210/pdb1g70/pdb
• Descriptor: HIV-1 RRE-IIB 32 NUCLEOTIDE RNA, RSG-1.2 PEPTIDE (2 entities in total)
• Functional Keywords: peptide-rna complex, non-canonical base pairs, viral protein-rna complex, viral protein/rna
• Biological source: Human immunodeficiency virus 1; More
• Total number of polymer chains: 2
• Total formula weight: 12918.09

Authors

Gosser, Y.,Hermann, T.,Majumdar, A.,Hu, W.,Frederick, R.,Jiang, F.,Xu, W.,Patel, D.J. (deposition date: 2000-11-08, release date: 2001-02-07, Last modification date: 2024-05-22)

Primary citation

Gosser, Y.,Hermann, T.,Majumdar, A.,Hu, W.,Frederick, R.,Jiang, F.,Xu, W.,Patel, D.J.
Peptide-triggered conformational switch in HIV-1 RRE RNA complexes.
Nat.Struct.Biol., 8:146-150, 2001

PubMed Abstract: We have used NMR spectroscopy to determine the solution structure of a complex between an oligonucleotide derived from stem IIB of the Rev responsive element (RRE-IIB) of HIV-1 mRNA and an in vivo selected, high affinity binding Arg-rich peptide. The peptide binds in a partially alpha-helical conformation into a pocket within the RNA deep groove. Comparison with the structure of a complex between an alpha-helical Rev peptide and RRE-IIB reveals that the sequence of the bound peptide determines the local conformation of the RRE peptide binding site. A conformational switch of an unpaired uridine base was revealed; this points out into the solvent in the Rev peptide complex, but it is stabilized inside the RNA deep groove by stacking with an Arg side chain in the selected peptide complex. The conformational switch has been visualized by NMR chemical shift mapping of the uridine H5/H6 atoms during a competition experiment in which Rev peptide was displaced from RRE-IIB by the higher affinity binding selected peptide.

PubMed: 11175904
DOI: 10.1038/84138

Experimental method

SOLUTION NMR