9GXX
70S ribosome with doublet-decoding tRNASer3 bound to A-site GCA codon
This is a non-PDB format compatible entry.
Summary for 9GXX
| Entry DOI | 10.2210/pdb9gxx/pdb |
| EMDB information | 51679 |
| Descriptor | 16S rRNA, Small ribosomal subunit protein uS10, Small ribosomal subunit protein uS11, ... (60 entities in total) |
| Functional Keywords | decoding, frame shift, translation, ribosome |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 56 |
| Total formula weight | 2236642.54 |
| Authors | Krishnaswamy, S.,Larsson, D.S.D.,Selmer, M. (deposition date: 2024-10-01, release date: 2025-05-28, Last modification date: 2025-12-24) |
| Primary citation | Krishnaswamy, S.,Akbar, S.,Larsson, D.S.D.,Chen, Y.,Selmer, M. Doublet decoding of tRNA Ser3 demonstrates plasticity of ribosomal decoding center. Nat Commun, 16:5402-5402, 2025 Cited by PubMed Abstract: Frameshifts can be caused by specific combinations of tRNA and mRNA. The wildtype AGC-decoding E. coli tRNA has been shown to induce -1 ribosomal frameshifting on GCA alanine codons, and proposed to read a two-base codon instead of a canonical triplet. However, it has remained unclear whether this type of non-cognate decoding can be accommodated by the ribosome. Here, we perform single-particle cryo-EM reconstructions on E. coli 70S ribosomes with the frameshift-inducing tRNA bound to the non-cognate GCA codon or the cognate AGC codon in the ribosomal A site. The structures demonstrate that doublet decoding is made possible when A1493, the conserved monitoring base in 16S rRNA, mimics a first codon base, forming a Hoogsteen base pair with U36 from the anticodon and stacking with the mRNA. This interaction pushes the first two bases of the A-site codon in position for base pairing with C35 and G34 of the anticodon. PubMed: 40571681DOI: 10.1038/s41467-025-61016-5 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.61 Å) |
Structure validation
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