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TitleTransfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 104, Issue 42, Page 16540-16545, Year 2007
Publish dateOct 16, 2007
AuthorsWen Li / Joachim Frank /
PubMed AbstractTransfer RNA (tRNA) transiently occupies the hybrid P/E state (P/E-tRNA) when mRNA-tRNA are translocated in the ribosome. In this study, we characterize the structure of P/E-tRNA and its interactions ...Transfer RNA (tRNA) transiently occupies the hybrid P/E state (P/E-tRNA) when mRNA-tRNA are translocated in the ribosome. In this study, we characterize the structure of P/E-tRNA and its interactions with the ribosome by correlating the results from molecular dynamics simulations on free tRNA with the cryo-EM map of P/E-tRNA. In our approach, we show that the cryo-EM map may be interpreted as a conformational average. Along the molecular dynamics trajectories (44 ns, 18 ns, and 18 ns), some of the snapshots prove to be quite close to the observed density. In a representative structure, the CCA (3') arm is uniquely twisted, and the anticodon stem loop is kinked at the junctions to both the anticodon loop and the D stem. In addition, the map shows that the P/E-tRNA is no longer bound to helix H69 of 23S rRNA and is flexible, and the conformations of helices H68 and h44 of 16S rRNA differ from those in the x-ray structure. Thus, our study presents structural and dynamic information on the P/E-tRNA and characterizes its interactions with the translocating ribosome.
External linksProc Natl Acad Sci U S A / PubMed:17925437 / PubMed Central
MethodsEM (single particle)
Resolution11.7 Å
Structure data

PDB-2z9q:
Transfer RNA in the hybrid P/E state
Method: ELECTRON MICROSCOPY / Resolution: 11.7 Å

Source
  • thermus aquaticus (bacteria)
KeywordsRNA / distorted anticodon-stem-loop / twisted CCA arm

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