SNAP output for PDB entry 1zho [SNAP web server]

PDB-id

1zho; SNAP-derived features in text and JSON formats; DNAproDB

Class

structural protein-RNA

Method

X-ray (2.6 Å)

Summary

The structure of a ribosomal protein l1 in complex with mrna

Reference

Nevskaya N, Tishchenko S, Volchkov S, Kljashtorny V, Nikonova E, Nikonov O, Nikulin A, Kohrer C, Piendl W, Zimmermann R, Stockley P, Garber M, Nikonov S (2006): "New insights into the interaction of ribosomal protein L1 with RNA." J.Mol.Biol., 355, 747-759. doi: 10.1016/j.jmb.2005.10.084.

Abstract

The RNA-binding ability of ribosomal protein L1 is of profound interest, since L1 has a dual function as a ribosomal structural protein that binds rRNA and as a translational repressor that binds its own mRNA. Here, we report the crystal structure at 2.6 A resolution of ribosomal protein L1 from the bacterium Thermus thermophilus in complex with a 38 nt fragment of L1 mRNA from Methanoccocus vannielii. The conformation of RNA-bound T.thermophilus L1 differs dramatically from that of the isolated protein. Analysis of four copies of the L1-mRNA complex in the crystal has shown that domain II of the protein does not contribute to mRNA-specific binding. A detailed comparison of the protein-RNA interactions in the L1-mRNA and L1-rRNA complexes identified amino acid residues of L1 crucial for recognition of its specific targets on the both RNAs. Incorporation of the structure of bacterial L1 into a model of the Escherichia coli ribosome revealed two additional contact regions for L1 on the 23S rRNA that were not identified in previous ribosome models.