Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV

J Mol Biol. 2011 Feb 4;405(5):1139-53. doi: 10.1016/j.jmb.2010.11.034. Epub 2010 Dec 9.


The structural mechanism by which nonstructural protein 3 (NS3) from the hepatitis C virus (HCV) translocates along RNA is currently unknown. HCV NS3 is an ATP-dependent motor protein essential for viral replication and a member of the superfamily 2 helicases. Crystallographic analysis using a labeled RNA oligonucleotide allowed us to unambiguously track the positional changes of RNA bound to full-length HCV NS3 during two discrete steps of the ATP hydrolytic cycle. The crystal structures of HCV NS3, NS3 bound to bromine-labeled RNA, and a tertiary complex of NS3 bound to labeled RNA and a non-hydrolyzable ATP analog provide a direct view of how large domain movements resulting from ATP binding and hydrolysis allow the enzyme to translocate along the phosphodiester backbone. While directional translocation of HCV NS3 by a single base pair per ATP hydrolyzed is observed, the 3' end of the RNA does not shift register with respect to a conserved tryptophan residue, supporting a "spring-loading" mechanism that leads to larger steps by the enzyme as it moves along a nucleic acid substrate.

Publication types

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

MeSH terms

  • Adenosine Triphosphatases / chemistry
  • Adenosine Triphosphate / chemistry
  • Crystallography
  • Hepacivirus / enzymology*
  • Humans
  • Protein Structure, Tertiary
  • RNA Helicases / chemistry*
  • RNA Transport*
  • Substrate Specificity
  • Viral Nonstructural Proteins / chemistry*


  • NS3 protein, hepatitis C virus
  • Viral Nonstructural Proteins
  • Adenosine Triphosphate
  • Adenosine Triphosphatases
  • RNA Helicases

Associated data

  • PDB/3O8B
  • PDB/3O8C
  • PDB/3O8D
  • PDB/3O8R