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A
Cryo‐EM density (mesh) and stick model of the nascent chain residues modeled in the 80S ribosome stalled on the CGA–CCG inhibitory codon pair. The density of the CGA‐encoded Arg of the first codon pair is clearly distinguishable as well as the bulky density of Trp65 of the uL4 encoded upstream in the translated mRNA construct.
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B
Cryo‐EM density (mesh) and stick model of the peptidyl‐transferase center as observed in the structure of ribosome stalled on the CGA–CCG inhibitory codon pair. Notably, for the U2875 (U2506 in E. coli), no clear density is observed, most likely due to enhanced flexibility. Yet, no directly observable major perturbation of the PTC components is apparent.
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C
Cryo‐EM density (mesh) and stick model with cartoon phosphate backbone representing the mRNA positions +1 to +4 and their interactions in the CGA–CCG‐stalled ribosome.
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D
Effect of flipped C+4 on the general path of the mRNA in the A site. A cartoon representation of mRNAs in all four discussed 80S structures is compared.
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E, F
Comparison between the A‐site tRNA decoding situation and the CGA–CCG‐stalled situation of the mRNA in positions +1 to +4. In the CGA–CCG A site, the C+4 is flipped by approximately 95° degrees toward the wobble A:I base pair and the mRNA backbone is shifted by 2.6 Å at the phosphate linking A+3 and C+4.
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G
Overview of the mRNA and its interactions in the A site of CGA–CCG reporter stalled ribosome using stick model with cartoon phosphate backbone representation. Sequence of mRNA positions +4 to +14 is CCGCGACCGUA.
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H
Detail of the tip of the hairpin from (G) with stabilizing stacking interactions between A2256 of the 25S rRNA and the C+7 of the mRNA and among A1756 of the 18S rRNA intercalated between the C+5 and the A+14 of the mRNA.
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I
Cryo‐EM density (mesh) and stick model with cartoon phosphate backbone representing the mRNA positions +1 to +4 and their interactions in the CGA–CGA‐stalled ribosome.
