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Structure paper

TitleStructural characterization of ribosome recruitment and translocation by type IV IRES.
Journal, issue, pagesElife, Vol. 5, Year 2016
Publish dateMay 9, 2016
AuthorsJason Murray / Christos G Savva / Byung-Sik Shin / Thomas E Dever / V Ramakrishnan / Israel S Fernández /
PubMed AbstractViral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps ...Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts tvhe otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation.
External linksElife / PubMed:27159451 / PubMed Central
MethodsEM (single particle)
Resolution3.6 - 3.8 Å
Structure data

8123

5it7

EMDB-8123, PDB-5it7:
Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2
Method: EM (single particle) / Resolution: 3.6 Å

8124

5it9

EMDB-8124, PDB-5it9:
Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES.
Method: EM (single particle) / Resolution: 3.8 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-GCP:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogue*YM

ChemComp-6EM:
(2S)-1-amino-N,N,N-trimethyl-1-oxobutan-2-aminium

Source
  • kluyveromyces lactis (yeast)
  • cricket paralysis virus
  • saccharomyces cerevisiae p283 (yeast)
  • Yeast (fungus)
  • Baker's yeast (brewer's yeast)
  • Kluyveromyces lacti (yeast)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
KeywordsRIBOSOME / translocation / IRES / eEF2 / small / subunit

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