Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of AUC codon discrimination during translation initiation in yeast.
Journal, issue, pages	Nucleic Acids Res, Vol. 52, Issue 18, Page 11317-11335, Year 2024
Publish date	Oct 14, 2024
Authors	Laura Villamayor-Belinchón / Prafful Sharma / Yuliya Gordiyenko / Jose L Llácer / Tanweer Hussain /
PubMed Abstract	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 ...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 links	Nucleic Acids Res / PubMed:39193907 / PubMed Central
Methods	EM (single particle)
Resolution	3.35 - 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 19808 8s8k EMDB-19808, PDB-8s8k: Structure of a yeast 48S-AUC preinitiation complex in swivelled conformation (model py48S-AUC-swiv-eIF1) Method: EM (single particle) / Resolution: 4.0 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogueYM 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)
Keywords	RIBOSOME / translation / initiation factors / 40S / eIF1A / AUC codon / eIF2 / tRNAi / 48S PIC / small ribosome subunit