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Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 S RNA

Brodersen, Ditlev E. and Clemons, William M., Jr. and Carter, Andrew P. and Wimberly, Brian T. and Ramakrishnan, V. (2002) Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 S RNA. Journal of Molecular Biology, 316 (3). pp. 725-768. ISSN 0022-2836. doi:10.1006/jmbi.2001.5359. https://resolver.caltech.edu/CaltechAUTHORS:20181030-134119635

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Abstract

We present a detailed analysis of the protein structures in the 30 S ribosomal subunit from Thermus thermophilus, and their interactions with 16 S RNA based on a crystal structure at 3.05 Å resolution. With 20 different polypeptide chains, the 30 S subunit adds significantly to our data base of RNA structure and protein-RNA interactions. In addition to globular domains, many of the proteins have long, extended regions, either in the termini or in internal loops, which make extensive contact to the RNA component and are involved in stabilizing RNA tertiary structure. Many ribosomal proteins share similar α+β sandwich folds, but we show that the topology of this domain varies considerably, as do the ways in which the proteins interact with RNA. Analysis of the protein-RNA interactions in the context of ribosomal assembly shows that the primary binders are globular proteins that bind at RNA multihelix junctions, whereas proteins with long extensions assemble later. We attempt to correlate the structure with a large body of biochemical and genetic data on the 30 S subunit.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1006/jmbi.2001.5359DOIArticle
ORCID:
AuthorORCID
Clemons, William M., Jr.0000-0002-0021-889X
Additional Information:© 2002 Elsevier. Received 11 September 2001, Revised 12 December 2001, Accepted 18 December 2001. This work was supported by the Medical Research Council (UK) and NIH grant GM44973 (to S. W. White and V. R). D. E. B. was the recipient of a Human Frontier Science Program postdoctoral fellowship, and W. M. C. received an NIH predoctoral fellowship. We thank R. Brimacombe, R.A. Zimmermann, F. V. Murphy, and K. Nagai for critically reading the manuscript and making useful suggestions, and P.R. Evans for advice on improving the Figures. Protein data bank accession code: Coordinates are available in the Protein Data Bank (http://www.rcsb.org) with accession ID 1FJF. Additional coordinates and information can be obtained from the 30 S website at http://alf1.mrc-lmb.cam. ac.uk/∼ribo/30 S
Funders:
Funding AgencyGrant Number
Medical Research Council (UK)UNSPECIFIED
NIHGM44973
Human Frontier Science ProgramUNSPECIFIED
NIH Predoctoral FellowshipUNSPECIFIED
Subject Keywords:30 S; ribosome; protein-RNA interactions; 16 S RNA; assembly
Issue or Number:3
DOI:10.1006/jmbi.2001.5359
Record Number:CaltechAUTHORS:20181030-134119635
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20181030-134119635
Official Citation:Ditlev E. Brodersen, William M. Clemons, Andrew P. Carter, Brian T. Wimberly, V. Ramakrishnan, Crystal structure of the 30 s ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 s RNA11Edited by R. Huber, Journal of Molecular Biology, Volume 316, Issue 3, 2002, Pages 725-768, ISSN 0022-2836, https://doi.org/10.1006/jmbi.2001.5359. (http://www.sciencedirect.com/science/article/pii/S0022283601953598)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:90514
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:30 Oct 2018 23:24
Last Modified:16 Nov 2021 03:33

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