The mechanism of RNA duplex recognition and unwinding by DEAD-box helicase DDX3X

Nat Commun. 2019 Jul 12;10(1):3085. doi: 10.1038/s41467-019-11083-2.


DEAD-box helicases (DDXs) regulate RNA processing and metabolism by unwinding short double-stranded (ds) RNAs. Sharing a helicase core composed of two RecA-like domains (D1D2), DDXs function in an ATP-dependent, non-processive manner. As an attractive target for cancer and AIDS treatment, DDX3X and its orthologs are extensively studied, yielding a wealth of biochemical and biophysical data, including structures of apo-D1D2 and post-unwound D1D2:single-stranded RNA complex, and the structure of a D2:dsRNA complex that is thought to represent a pre-unwound state. However, the structure of a pre-unwound D1D2:dsRNA complex remains elusive, and thus, the mechanism of DDX action is not fully understood. Here, we describe the structure of a D1D2 core in complex with a 23-base pair dsRNA at pre-unwound state, revealing that two DDXs recognize a 2-turn dsRNA, each DDX mainly recognizes a single RNA strand, and conformational changes induced by ATP binding unwinds the RNA duplex in a cooperative manner.

Publication types

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

MeSH terms

  • DEAD-box RNA Helicases / isolation & purification
  • DEAD-box RNA Helicases / metabolism
  • DEAD-box RNA Helicases / ultrastructure*
  • RNA, Double-Stranded / metabolism*
  • Recombinant Proteins / isolation & purification
  • Recombinant Proteins / metabolism
  • Recombinant Proteins / ultrastructure
  • Scattering, Small Angle
  • Substrate Specificity
  • X-Ray Diffraction


  • RNA, Double-Stranded
  • Recombinant Proteins
  • DDX3X protein, human
  • DEAD-box RNA Helicases