title: The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure.
abstract: Bacterial class I release factors (RFs) are seen by cryo-electron microscopy (cryo-EM) to span the distance between the ribosomal decoding and peptidyl transferase centers during translation termination. The compact conformation of bacterial RF1 and RF2 observed in crystal structures will not span this distance, and large structural rearrangements of RFs have been suggested to play an important role in termination. We have collected small-angle X-ray scattering (SAXS) data from E. coli RF1 and from a functionally active truncated RF1 derivative. Theoretical scattering curves, calculated from crystal and cryo-EM structures, were compared with the experimental data, and extensive analyses of alternative conformations were made. Low-resolution models were constructed ab initio, and by rigid-body refinement using RF1 domains. The SAXS data were compatible with the open cryo-EM conformation of ribosome bound RFs and incompatible with the crystal conformation. These conclusions obviate the need for assuming large conformational changes in RFs during termination.
authors.affiliation: Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Copenhagen.
authors.forename: Bente
authors.initials: B
authors.lastname: Vestergaard
authors.forename: Suparna
authors.initials: S
authors.lastname: Sanyal
authors.forename: Manfred
authors.initials: M
authors.lastname: Roessle
authors.forename: Liliana
authors.initials: L
authors.lastname: Mora
authors.forename: Richard H
authors.initials: RH
authors.lastname: Buckingham
authors.forename: Jette S
authors.initials: JS
authors.lastname: Kastrup
authors.forename: Michael
authors.initials: M
authors.lastname: Gajhede
authors.forename: Dmitri I
authors.initials: DI
authors.lastname: Svergun
authors.forename: Måns
authors.initials: M
authors.lastname: Ehrenberg
mesh_terms: D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D010454:Peptide Termination Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; D010454:Peptide Termination Factors; C489005:prfA protein, E coli