3A3A

Crystal structure of human selenocystine tRNA

Summary for 3A3A

• Entry DOI: 10.2210/pdb3a3a/pdb
• Descriptor: selenocysteine tRNA (1 entity in total)
• Functional Keywords: trna, rna
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 28908.08

Authors

Itoh, Y.,Chiba, S.,Sekine, S.I.,Yokoyama, S. (deposition date: 2009-06-11, release date: 2009-08-11, Last modification date: 2023-11-01)

Primary citation

Itoh, Y.,Chiba, S.,Sekine, S.,Yokoyama, S.
Crystal structure of human selenocysteine tRNA.
Nucleic Acids Res., 37:6259-6268, 2009

PubMed Abstract: Selenocysteine (Sec) is the 21st amino acid in translation. Sec tRNA (tRNA(Sec)) has an anticodon complementary to the UGA codon. We solved the crystal structure of human tRNA(Sec). tRNA(Sec) has a 9-bp acceptor stem and a 4-bp T stem, in contrast with the 7-bp acceptor stem and the 5-bp T stem in the canonical tRNAs. The acceptor stem is kinked between the U6:U67 and G7:C66 base pairs, leading to a bent acceptor-T stem helix. tRNA(Sec) has a 6-bp D stem and a 4-nt D loop. The long D stem includes unique A14:U21 and G15:C20a pairs. The D-loop:T-loop interactions include the base pairs G18:U55 and U16:U59, and a unique base triple, U20:G19:C56. The extra arm comprises of a 6-bp stem and a 4-nt loop. Remarkably, the D stem and the extra arm do not form tertiary interactions in tRNA(Sec). Instead, tRNA(Sec) has an open cavity, in place of the tertiary core of a canonical tRNA. The linker residues, A8 and U9, connecting the acceptor and D stems, are not involved in tertiary base pairing. Instead, U9 is stacked on the first base pair of the extra arm. These features might allow tRNA(Sec) to be the target of the Sec synthesis/incorporation machineries.

PubMed: 19692584
DOI: 10.1093/nar/gkp648

Experimental method

X-RAY DIFFRACTION (3.1 Å)