6GSK
Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and near-cognate tRNAThr in the A-site
This is a non-PDB format compatible entry.
Summary for 6GSK
| Entry DOI | 10.2210/pdb6gsk/pdb |
| Descriptor | 16S ribosomal RNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (58 entities in total) |
| Functional Keywords | translation, ribosome, decoding |
| Biological source | Thermus thermophilus HB8 More |
| Total number of polymer chains | 107 |
| Total formula weight | 4501172.99 |
| Authors | Rozov, A.,Yusupov, M.,Yusupova, G. (deposition date: 2018-06-14, release date: 2018-07-04, Last modification date: 2024-01-17) |
| Primary citation | Rozov, A.,Wolff, P.,Grosjean, H.,Yusupov, M.,Yusupova, G.,Westhof, E. Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria. Nucleic Acids Res., 46:7425-7435, 2018 Cited by PubMed Abstract: We report new crystallographic structures of Thermus thermophilus ribosomes complexed with long mRNAs and native Escherichia coli tRNAs. They complete the full set of combinations of Watson-Crick G•C and miscoding G•U pairs at the first two positions of the codon-anticodon duplex in ribosome functional complexes. Within the tight decoding center, miscoding G•U pairs occur, in all combinations, with a non-wobble geometry structurally indistinguishable from classical coding Watson-Crick pairs at the same first two positions. The contacts with the ribosomal grip surrounding the decoding center are all quasi-identical, except in the crowded environment of the amino group of a guanosine at the second position; in which case a G in the codons may be preferred. In vivo experimental data show that the translational errors due to miscoding by G•U pairs at the first two positions are the most frequently encountered ones, especially at the second position and with a G on the codon. Such preferred miscodings involve a switch from an A-U to a G•U pair in the tRNA/mRNA complex and very rarely from a G = C to a G•U pair. It is concluded that the frequencies of such occurrences are only weakly affected by the codon/anticodon structures but depend mainly on the stability and lifetime of the complex, the modifications present in the anticodon loop, especially those at positions 34 and 37, in addition to the relative concentration of cognate/near-cognate tRNA species present in the cellular tRNA pool. PubMed: 29931292DOI: 10.1093/nar/gky547 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.36 Å) |
Structure validation
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