Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography

J Mol Biol. 2010 Dec 17;404(5):751-72. doi: 10.1016/j.jmb.2010.09.009. Epub 2010 Oct 8.


The 5'-untranslated regions of all gammaretroviruses contain a conserved "double-hairpin motif" (Ψ(CD)) that is required for genome packaging. Both hairpins (SL-C and SL-D) contain GACG tetraloops that, in isolated RNAs, are capable of forming "kissing" interactions stabilized by two intermolecular G-C base pairs. We have determined the three-dimensional structure of the double hairpin from the Moloney murine leukemia virus ([Ψ(CD)](2), 132 nt, 42.8 kDa) using a (2)H-edited NMR-spectroscopy-based approach. This approach enabled the detection of (1)H-(1)H dipolar interactions that were not observed in previous studies of isolated SL-C and SL-D hairpin RNAs using traditional (1)H-(1)H correlated and (1)H-(13)C-edited NMR methods. The hairpins participate in intermolecular cross-kissing interactions (SL-C to SL-D' and SLC' to SL-D) and stack in an end-to-end manner (SL-C to SL-D and SL-C' to SL-D') that gives rise to an elongated overall shape (ca 95 Å×45 Å×25 Å). The global structure was confirmed by cryo-electron tomography (cryo-ET), making [Ψ(CD)](2) simultaneously the smallest RNA to be structurally characterized to date by cryo-ET and among the largest to be determined by NMR. Our findings suggest that, in addition to promoting dimerization, [Ψ(CD)](2) functions as a scaffold that helps initiate virus assembly by exposing a cluster of conserved UCUG elements for binding to the cognate nucleocapsid domains of assembling viral Gag proteins.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions*
  • Animals
  • Cryoelectron Microscopy
  • Dimerization
  • Electron Microscope Tomography
  • Magnetic Resonance Spectroscopy
  • Models, Biological
  • Models, Molecular
  • Moloney murine leukemia virus / chemistry*
  • Moloney murine leukemia virus / physiology
  • Nucleic Acid Conformation
  • RNA, Viral / chemistry*
  • RNA, Viral / metabolism*
  • Virus Assembly*


  • 5' Untranslated Regions
  • RNA, Viral

Associated data

  • PDB/2L1F