Model for the Three-Dimensional Folding of 16s Ribosomal Rna

Stern, S., Weiser, B., Noller, H. F. (November 1988) Model for the Three-Dimensional Folding of 16s Ribosomal Rna. Journal of Molecular Biology, 204 (2). pp. 447-482. ISSN 0022-2836

URL: https://www.ncbi.nlm.nih.gov/pubmed/2464693
DOI: 10.1016/0022-2836(88)90588-8

Abstract

We have derived a model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA, using interactive computer graphic methods. It is based on (1) the secondary structure derived from comparative sequence analysis, (2) the three-dimensional co-ordinates for the centers of mass of the 30 S subunit proteins, and (3) the locations of sites in 16 S rRNA that interact with specific ribosomal proteins, from footprinting and crosslinking studies. We present a detailed description of the derivation of the model. About 75% of the RNA chain is sufficiently constrained to provide a useful model. This contains most of the universally conserved core of the molecule. In all but a few instances, protected and crosslinked sites can be placed within or very close to their cognate proteins, while obeying stereochemical rules. The overall shape of the model and locations of specific regions of the RNA correspond well to data derived from electron micrographs of 30 S subunits, although such data were not used to construct the model. Phylogenetic variations in the structure are readily accommodated; as an example, we have modeleled the 950-nucleotide mammalian mitochondrial 12 S rRNA by superimposing it on the E. coli structure. The three major RNA domains, as defined by secondary structure, appear to exist as autonomous structural units in three dimensions, for the most part. There is an extensive interface between the 5' and central domains, whereas the 3' major domain has relatively little apparent contact with the rest of the structure. The 5', central and 3' major domains form structures that resemble the body, platform and head, respectively, seen in electron micrographs of 30 S subunits. We discuss possibleroles for the ribosomal proteins in stabilizing specific structural features of the RNA during ribosoma assembly. The decoding site, as deduced from footprinting and crosslinking studies involving the tRNA anticodon stemp-loop, is well-localized. Bases protected from chemical probing by the anticodon stem-loop line the cleft of the subunit. The conserved loop at position 530, which contains some of the bases protected by A site-bound tRNA, is remote (approx. 80 .ANG.) from the decoding site. Protection of these bases by the anticodon stem-loop is thus unlikely to be due to direct contact.

Item Type: Paper
Subjects: organism description > bacteria > escherichia coli
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > srRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > tRNA
CSHL Authors:
Communities: CSHL labs
Depositing User: Gail Sherman
Date: 20 November 1988
Date Deposited: 18 Sep 2017 16:30
Last Modified: 18 Sep 2017 16:30
Related URLs:
URI: http://repository.cshl.edu/id/eprint/35217

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