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Structure paper

TitleStructural studies of nedicistrovirus IRES-driven, initiation factor-independent translation shed light on key steps of eukaryotic translation elongation.
Journal, issue, pagesNucleic Acids Res, Vol. 54, Issue 10, Year 2026
Publish dateMay 20, 2026
AuthorsSwastik De / Clara G Altomare / Irina S Abaeva / Prikshat Dadhwal / Priyanka Garg / Francisco Acosta-Reyes / Zuben P Brown / Tatyana V Pestova / Christopher U T Hellen / Joachim Frank /
PubMed AbstractWe utilized the nedicistrovirus (NediV) intergenic region (IGR) internal ribosomal entry site (IRES)-mediated, initiation factor-independent translation initiation system and determined high- ...We utilized the nedicistrovirus (NediV) intergenic region (IGR) internal ribosomal entry site (IRES)-mediated, initiation factor-independent translation initiation system and determined high-resolution structures of 80S ribosome complexes with the NediV IRES in various functional states, including binary complexes, aminoacyl-transfer RNA (tRNA)-bound complexes, and complexes with elongation factor eEF2. In binary complexes, the NediV IRES primarily occupies the ribosomal P site, exhibiting conformational flexibility and engaging the ribosome at multiple interaction sites. Upon translocation, the IRES undergoes structural rearrangements, including destabilization of its PKI domain, facilitating the transition to canonical elongation. Crucially, we captured an eEF2-bound complex, along with an eEF1A-bound failed decoding complex featuring a mismatched tRNA, the latter representing the first instance of a canonical elongation complex visualized in the presence of a natural, hydrolysable nucleotide and without the addition of any trapping agents. These findings provide a comprehensive structural overview of IGR IRES-mediated translation initiation and its transition to elongation, revealing key mechanistic details of viral translation and proofreading.
External linksNucleic Acids Res / PubMed:42240621 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 4.1 Å
Structure data

72136

9q1q

EMDB-72136, PDB-9q1q:
NediV IRES (A site) in complex with Rabbit 80S ribosome
Method: EM (single particle) / Resolution: 3.5 Å

72137

9q1s

EMDB-72137, PDB-9q1s:
NediV IRES (P site) in complex with Rabbit 80S ribosome
Method: EM (single particle) / Resolution: 3.0 Å

72168

9q2m

EMDB-72168, PDB-9q2m:
Rabbit ribosomal 80S elongation complex with eEF2, partial P site Ala-tRNA, E site Ala-tRNA on NediV ORF
Method: EM (single particle) / Resolution: 3.3 Å

72171

9q2p

EMDB-72171, PDB-9q2p:
Rabbit ribosomal 80S elongation complex with eEF1A, A*/T Ala-tRNA, P site Ala-tRNA, E site Ala-tRNA on NediV ORF
Method: EM (single particle) / Resolution: 3.0 Å

72175

9q2t

EMDB-72175, PDB-9q2t:
NediV IRES in complex with Rabbit 80S ribosome with eEF2 and P site Ala-tRNA
Method: EM (single particle) / Resolution: 4.1 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

Source
  • nedicistrovirus tfn-2012
  • oryctolagus cuniculus (rabbit)
KeywordsRIBOSOME / IRES / Translation / Initiation

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