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J. Biol. Chem., Vol. 275, Issue 40, 31283-31288, October 6, 2000

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Structure of Free Thermus flavus 5 S rRNA at 1.3 nm Resolution from Synchrotron X-ray Solution Scattering^*

Sergio S. Funari, Gert Rapp, Markus Perbandt, Karsten Dierks^§, Marco Vallazza^¶, Christian Betzel, Volker A. Erdmann^¶, and Dmitri I. Svergun^**

From the   Institute of Physiological Chemistry, University Hospital Hamburg, c/o Deutsches Elektronen Synchrotron, Building 22a, Notkestrae 85, 22603 Hamburg, Germany, the ^§ Dierks and Partner Systemtechnologie, Pinneberger Weg 22-24, 20257 Hamburg, Germany, the ^¶ Institute of Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany, the ^** European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen Synchrotron, Notkestrae 85, 22603 Hamburg, Germany, and the  Institute of Crystallography, Russian Academy of Sciences, Leninsky prospect 59, 117333 Moscow, Russia

The shape of free Thermus flavus 5 S rRNA in solution at 1.3 nm resolution is restored from synchrotron x-ray scattering data using an ab initio simulated annealing algorithm. The free 5 S rRNA is a bent elongated molecule displaying a compact central region and two projecting arms, similar to those of the tRNA. The atomic models of the 5 S rRNA domains A-D-E and B-C in the form of elongated helices can be well accommodated within the shape, yielding a tentative model of the structure of the free 5 S rRNA in solution. Its comparison with the recent protein-RNA map in the ribosome (Svergun, D. I., and Nierhaus, K. H. (2000) J. Biol. Chem. 275, 14432-14439) indicates that the 5 S rRNA becomes essentially more compact upon complex formation with specific ribosomal proteins. A conceivable conformational change involves rotation of the B-C domain toward the A-D-E domain. The model of free 5 S rRNA displays no interactions between domains E and C, but such interactions are possible in the bound molecule.

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