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Structure of the ribosomal protein L1-mRNA complex at 2.1 A resolution: common features of crystal packing of L1-RNA complexes.

Tishchenko S, Nikonova E, Nikulin A, Nevskaya N, Volchkov S, Piendl W, Garber M, Nikonov S
Acta Crystallogr D Biol Crystallogr 62 1545-54 (2006)
Cited: 19 times
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Abstract

The crystal structure of a hybrid complex between the bacterial ribosomal protein L1 from Thermus thermophilus and a Methanococcus vannielii mRNA fragment containing an L1-binding site was determined at 2.1 A resolution. It was found that all polar atoms involved in conserved protein-RNA hydrogen bonds have high values of density in the electron-density map and that their hydrogen-bonding capacity is fully realised through interactions with protein atoms, water molecules and K(+) ions. Intermolecular contacts were thoroughly analyzed in the present crystals and in crystals of previously determined L1-RNA complexes. It was shown that extension of the RNA helices providing canonical helix stacking between open-open or open-closed ends of RNA fragments is a common feature of these and all known crystals of complexes between ribosomal proteins and RNAs. In addition, the overwhelming majority of complexes between ribosomal proteins and RNA molecules display crystal contacts formed by the central parts of the RNA fragments. These contacts are often very extensive and strong and it is proposed that they are formed in the saturated solution prior to crystal formation.

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Articles citing this publication (6)

  1. Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs. Olson WK, Li S, Kaukonen T, Colasanti AV, Xin Y, Lu XJ. Biochemistry 58 2474-2487 (2019)
  2. Domain II of Thermus thermophilus ribosomal protein L1 hinders recognition of its mRNA. Tishchenko S, Kljashtorny V, Kostareva O, Nevskaya N, Nikulin A, Gulak P, Piendl W, Garber M, Nikonov S. J Mol Biol 383 301-305 (2008)
  3. High-resolution crystal structure of the isolated ribosomal L1 stalk. Tishchenko S, Gabdulkhakov A, Nevskaya N, Sarskikh A, Kostareva O, Nikonova E, Sycheva A, Moshkovskii S, Garber M, Nikonov S. Acta Crystallogr D Biol Crystallogr 68 1051-1057 (2012)
  4. Protein-RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions. Tishchenko S, Kostareva O, Gabdulkhakov A, Mikhaylina A, Nikonova E, Nevskaya N, Sarskikh A, Piendl W, Garber M, Nikonov S. Acta Crystallogr D Biol Crystallogr 71 376-386 (2015)
  5. A structure-based model for the prediction of protein-RNA binding affinity. Nithin C, Mukherjee S, Bahadur RP. RNA 25 1628-1645 (2019)
  6. Studying the properties of domain I of the ribosomal protein l1: incorporation into ribosome and regulation of the l1 operon expression. Korepanov AP, Kostareva OS, Bazhenova MV, Bubunenko MG, Garber MB, Tishchenko SV. Protein J 34 103-110 (2015)


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