title: Structure of free Thermus flavus 5 S rRNA at 1.3 nm resolution from synchrotron X-ray solution scattering.
abstract: 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.
authors.affiliation: Institute of Physiological Chemistry, University Hospital Hamburg, c/o Deutsches Elektronen Synchrotron, Building 22a, Notkestrabetae 85, 22603 Hamburg, Germany.
authors.forename: S S
authors.initials: SS
authors.lastname: Funari
authors.forename: G
authors.initials: G
authors.lastname: Rapp
authors.forename: M
authors.initials: M
authors.lastname: Perbandt
authors.forename: K
authors.initials: K
authors.lastname: Dierks
authors.forename: M
authors.initials: M
authors.lastname: Vallazza
authors.forename: C
authors.initials: C
authors.lastname: Betzel
authors.forename: V A
authors.initials: VA
authors.lastname: Erdmann
authors.forename: D I
authors.initials: DI
authors.lastname: Svergun
mesh_terms: D000465:Algorithms; D004305:Dose-Response Relationship, Drug; D004926:Escherichia coli / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012341:RNA, Ribosomal, 5S / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry; D012542:Scattering, Radiation; D012984:Software; D013824:Thermus / Q000737:chemistry* / Q000235:genetics*; D014965:X-Rays
chemical_list: D012341:RNA, Ribosomal, 5S