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TitleStructural basis of AUC codon discrimination during translation initiation in yeast.
Journal, issue, pagesNucleic Acids Res, Year 2024
Publish dateAug 28, 2024
AuthorsLaura Villamayor-Belinchón / Prafful Sharma / Yuliya Gordiyenko / Jose L Llácer / Tanweer Hussain /
PubMed AbstractIn eukaryotic translation initiation, the 48S preinitiation complex (PIC) scans the 5' untranslated region of mRNAs to search for the cognate start codon (AUG) with assistance from various ...In eukaryotic translation initiation, the 48S preinitiation complex (PIC) scans the 5' untranslated region of mRNAs to search for the cognate start codon (AUG) with assistance from various eukaryotic initiation factors (eIFs). Cognate start codon recognition is precise, rejecting near-cognate codons with a single base difference. However, the structural basis of discrimination of near-cognate start codons was not known. We have captured multiple yeast 48S PICs with a near-cognate AUC codon at the P-site, revealing that the AUC codon induces instability in the codon-anticodon at the P-site, leading to a disordered N-terminal tail of eIF1A. Following eIF1 dissociation, the N-terminal domain of eIF5 fails to occupy the vacant eIF1 position, and eIF2β becomes flexible. Consequently, 48S with an AUC codon is less favourable for initiation. Furthermore, we observe hitherto unreported metastable states of the eIF2-GTP-Met-tRNAMet ternary complex, where the eIF2β helix-turn-helix domain may facilitate eIF5 association by preventing eIF1 rebinding to 48S PIC. Finally, a swivelled head conformation of 48S PIC appears crucial for discriminating incorrect and selection of the correct codon-anticodon pair during translation initiation.
External linksNucleic Acids Res / PubMed:39193907
MethodsEM (single particle)
Resolution3.35 - 4.7 Å
Structure data

19541

8rw1

EMDB-19541, PDB-8rw1:
Structure of a yeast 48S-AUC preinitiation complex in closed conformation
Method: EM (single particle) / Resolution: 3.35 Å

19801

8s8d

EMDB-19801, PDB-8s8d:
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2)
Method: EM (single particle) / Resolution: 3.45 Å

19802

8s8e

EMDB-19802, PDB-8s8e:
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.1)
Method: EM (single particle) / Resolution: 3.85 Å

19803

8s8f

EMDB-19803, PDB-8s8f:
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.2)
Method: EM (single particle) / Resolution: 3.95 Å

19804

8s8g

EMDB-19804, PDB-8s8g:
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2.1)
Method: EM (single particle) / Resolution: 4.0 Å

19805

8s8h

EMDB-19805, PDB-8s8h:
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2.2)
Method: EM (single particle) / Resolution: 4.0 Å

19806

8s8i

EMDB-19806, PDB-8s8i:
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF1)
Method: EM (single particle) / Resolution: 4.3 Å

19807

8s8j

EMDB-19807, PDB-8s8j:
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF5)
Method: EM (single particle) / Resolution: 4.7 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

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

ChemComp-MET:
METHIONINE

ChemComp-HOH:
WATER

Source
  • Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
  • Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
  • kluyveromyces lactis (yeast)
  • kluyveromyces lactis nrrl y-1140 (yeast)
  • saccharomyces cerevisiae s288c (yeast)
KeywordsRIBOSOME / translation / initiation factors / 40S / eIF1A / AUC codon / eIF2 / tRNAi / 48S PIC / small ribosome subunit

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