Interactions and dynamics of the Shine-Dalgarno helix in the 70S ribosome

The crystal structure of an initiation-like 70S ribosome complex containing an 8-bp Shine-Dalgarno (SD) helix was determined at 3.8-Å resolution. Translation-libration-screw analysis showed that the inherent anisotropic motions of the SD helix were biased along its helical axis, suggesting that duri...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2007-10, Vol.104 (43), p.16840-16843
Main Authors: Korostelev, Andrei, Trakhanov, Sergei, Asahara, Haruichi, Laurberg, Martin, Lancaster, Laura, Noller, Harry F
Format: Article
Language:English
Subjects:
Anisotropy
Archaea
Base Sequence
Biochemistry
Biological Sciences
Crystal structure
Crystallization
Crystallography, X-Ray
Crystals
Data collection
Electron density
Messenger RNA
Models, Molecular
Molecular Sequence Data
Nucleic Acid Conformation
Nucleotides
Regulatory Sequences, Ribonucleic Acid - genetics
Ribonucleic acid
Ribosomes
Ribosomes - metabolism
RNA
RNA, Bacterial - chemistry
RNA, Bacterial - metabolism
Start codon
Thermus thermophilus - metabolism
Transfer RNA
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Summary:The crystal structure of an initiation-like 70S ribosome complex containing an 8-bp Shine-Dalgarno (SD) helix was determined at 3.8-Å 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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0707850104