Preformed protein-binding motifs in 7SK snRNA: structural and thermodynamic comparisons with retroviral TAR

J Mol Biol. 2010 Dec 10;404(4):555-67. doi: 10.1016/j.jmb.2010.08.042. Epub 2010 Sep 15.


The 7SK small nuclear RNA is a highly conserved non-coding RNA that regulates transcriptional elongation. 7SK utilizes the HEXIM proteins to sequester the transcription factor P-TEFb by a mechanism similar to that used by retroviral TAR RNA to engage Tat and P-TEFb. Tat has also recently been shown to bind 7SK directly and recruit P-TEFb to TAR. We report here the solution structures of the free and arginine-bound forms of stem loop 4 of 7SK (7SK-SL4). Comparison of the 7SK-SL4 and TAR structures demonstrates the presence of a common arginine sandwich motif. However, arginine binding to 7SK-SL4 is mechanistically distinct and occurs via docking into a pre-organized pocket resulting in a 1000-fold increased affinity. Furthermore, whereas formation of the binding pocket in TAR requires a critical base-triple, hydrogen-bond formation between the equivalent bases in 7SK-SL4 is not essential and the pocket is stabilized solely by a pseudo base-triple platform. In addition, this theme of preformed protein binding motifs also extends into the pentaloop. The configuration of the loop suggests that 7SK-SL4 is poised to make ternary contacts with P-TEFb and HEXIM or Tat. These key differences between 7SK-SL4 and TAR present an opportunity to understand RNA structural adaptation and have implications for understanding differential interactions with Tat.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • HIV Long Terminal Repeat
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Nucleic Acid Conformation
  • Positive Transcriptional Elongation Factor B / chemistry*
  • Positive Transcriptional Elongation Factor B / metabolism*
  • Protein Binding
  • RNA, Small Nuclear / chemistry*
  • RNA, Small Nuclear / metabolism*
  • Thermodynamics


  • RNA, Small Nuclear
  • Positive Transcriptional Elongation Factor B

Associated data

  • PDB/2KX8