The structure of the HIV-1 RRE high affinity rev binding site at 1.6 A resolution

J Mol Biol. 2000 Jan 28;295(4):711-7. doi: 10.1006/jmbi.1999.3405.

Abstract

The crystal structure of a 28 nt RNA fragment containing the human immunodeficiency virus type 1 (HIV-1) Rev response element high affinity binding site for Rev protein has been solved at 1.6 A resolution. The overall structure of the RRE helix is greatly distorted from A-form geometry by the presence of two purine-purine base-pairs and two single nucleotide bulges. G48 and G71 form a Hoogsteen-type asymmetric base-pair with G71 adopting a syn conformation. The non-canonical regions in the unliganded Rev response element molecule narrow the major groove width with respect to standard A-RNA. The Rev response element structure observed here represents a closed form of the Rev binding site and differs from conformations of the RNA observed previously by solution NMR studies.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Crystallography, X-Ray / methods
  • HIV-1 / genetics*
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleic Acid Conformation*
  • RNA, Viral / chemistry*

Substances

  • RNA, Viral