Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome

Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1839-44. doi: 10.1073/pnas.1018582108. Epub 2011 Jan 18.

Abstract

Internal ribosome entry site (IRES) RNAs are elements of viral or cellular mRNAs that bypass steps of canonical eukaryotic cap-dependent translation initiation. Understanding of the structural basis of IRES mechanisms is limited, partially due to a lack of high-resolution structures of IRES RNAs bound to their cellular targets. Prompted by the universal phylogenetic conservation of the ribosomal P site, we solved the crystal structures of proposed P site binding domains from two intergenic region IRES RNAs bound to bacterial 70S ribosomes. The structures show that these IRES domains nearly perfectly mimic a tRNA • mRNA interaction. However, there are clear differences in the global shape and position of this IRES domain in the intersubunit space compared to those of tRNA, supporting a mechanism for IRES action that invokes hybrid state mimicry to drive a noncanonical mode of translocation. These structures suggest how relatively small structured RNAs can manipulate complex biological machines.

Publication types

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

MeSH terms

  • Base Sequence
  • Crystallization
  • Models, Molecular
  • Nucleic Acid Conformation
  • Phylogeny
  • RNA, Viral / chemistry
  • RNA, Viral / metabolism*
  • Ribosomes / metabolism*

Substances

  • RNA, Viral

Associated data

  • PDB/3PYN
  • PDB/3PYO
  • PDB/3PYQ
  • PDB/3PYR
  • PDB/3PYS
  • PDB/3PYT
  • PDB/3PYU
  • PDB/3PYV