title: Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.
abstract: The crystal structure of an initiation-like 70S ribosome complex containing an 8-bp Shine-Dalgarno (SD) helix was determined at 3.8-A resolution. Translation-libration-screw analysis showed that the inherent anisotropic motions of the SD helix were biased along its helical axis, suggesting that during the first step of translocation, the SD helix moves along its helical screw axis. Contacts between the SD helix and the ribosome were primarily through interactions with helices 23a, 26, and 28 of 16S rRNA. Contact with the neck (helix 28) of the 30S subunit near its hinge point suggests that formation of the SD helix could affect positioning of the head of the 30S subunit for optimal interaction with initiator tRNA. The bulged U723 in helix 23a interacts with the minor groove of the SD helix at the C1539.G-10 base pair, explaining its selective conservation in bacteria and archaea.
authors.affiliation: Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95060, USA.
authors.forename: Andrei
authors.initials: A
authors.lastname: Korostelev
authors.forename: Sergei
authors.initials: S
authors.lastname: Trakhanov
authors.forename: Haruichi
authors.initials: H
authors.lastname: Asahara
authors.forename: Martin
authors.initials: M
authors.lastname: Laurberg
authors.forename: Laura
authors.initials: L
authors.lastname: Lancaster
authors.forename: Harry F
authors.initials: HF
authors.lastname: Noller
mesh_terms: D001483:Base Sequence; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism*; D038621:Regulatory Sequences, Ribonucleic Acid / Q000235:genetics*; D012270:Ribosomes / Q000378:metabolism*; D016963:Thermus thermophilus / Q000378:metabolism*
chemical_list: D012329:RNA, Bacterial; D038621:Regulatory Sequences, Ribonucleic Acid