7EQJ

crystal structure of E. coli Valine tRNA

Summary for 7EQJ

• Entry DOI: 10.2210/pdb7eqj/pdb
• Descriptor: RNA (76-MER), MAGNESIUM ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: trna, rna
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 49204.93

Authors

Kim, J.,Jeong, H. (deposition date: 2021-05-03, release date: 2022-01-19, Last modification date: 2023-11-29)

Primary citation

Jeong, H.,Kim, J.
Unique anticodon loop conformation with the flipped-out wobble nucleotide in the crystal structure of unbound tRNA Val .
Rna, 27:1330-1338, 2021

PubMed Abstract: During protein synthesis on ribosome, tRNA recognizes its cognate codon of mRNA through base-pairing with the anticodon. The 5'-end nucleotide of the anticodon is capable of wobble base-pairing, offering a molecular basis for codon degeneracy. The wobble nucleotide is often targeted for post-transcriptional modification, which affects the specificity and fidelity of the decoding process. Flipping-out of a wobble nucleotide in the anticodon loop has been proposed to be necessary for modifying enzymes to access the target nucleotide, which has been captured in selective structures of protein-bound complexes. Meanwhile, all other structures of free or ribosome-bound tRNA display anticodon bases arranged in stacked conformation. We report the X-ray crystal structure of unbound tRNA to a 2.04 Å resolution showing two different conformational states of wobble uridine in the anticodon loop, one stacked on the neighboring base and the other swiveled out toward solvent. In addition, the structure reveals a rare magnesium ion coordination to the nitrogen atom of a nucleobase, which has been sampled very rarely among known structures of nucleic acids.

PubMed: 34315814
DOI: 10.1261/rna.078863.121

Experimental method

X-RAY DIFFRACTION (2.043 Å)