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Another piece of the ribosome: solution structure of S16 and its location in the 30S subunit

Allard, Peter and Rak, Alexey V. and Wimberly, Brian T. and Clemons, William M., Jr. and Kalinin, Alexander and Helgstrand, Magnus and Garber, Maria B. and Ramakrishnan, V. and Härd, Torleif (2000) Another piece of the ribosome: solution structure of S16 and its location in the 30S subunit. Structure, 8 (8). pp. 875-882. ISSN 0969-2126. https://resolver.caltech.edu/CaltechAUTHORS:20181029-110214031

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Abstract

Background: X-ray crystallography has recently yielded much-improved electron-density maps of the bacterial ribosome and its two subunits and many structural details of bacterial ribosome subunits are now being resolved. One approach to complement the structures and elucidate the details of rRNA and protein packing is to determine structures of individual protein components and model these into existing intermediate resolution electron density. Results: We have determined the solution structure of the ribosomal protein S16 from Thermus thermophilus. S16 is a mixed α/β protein with a novel folding scaffold based on a five-stranded antiparallel/parallel β sheet. Three large loops, which are partially disordered, extend from the sheet and two α helices are packed against its concave surface. Calculations of surface electrostatic potentials show a large continuous area of positive electrostatic potential and smaller areas of negative potential. S16 was modeled into a 5.5 Å electron-density map of the T. thermophilus 30S ribosomal subunit. Conclusions: The location and orientation of S16 in a narrow crevice formed by helix 21 and several other unassigned rRNA helices is consistent with electron density corresponding to the shape of S16, hydroxyl radical protection data, and the electrostatic surface potential of S16. Two protein neighbors to S16 are S4 and S20, which facilitate binding of S16 to the 30S subunit. Overall, this work exemplifies the benefits of combining high-resolution nuclear magnetic resonance (NMR) structures of individual components with low-resolution X-ray maps to elucidate structures of large complexes.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1016/s0969-2126(00)00177-5DOIArticle
ORCID:
AuthorORCID
Clemons, William M., Jr.0000-0002-0021-889X
Additional Information:© 2000 Elsevier Science Ltd. Received 17 April 2000, Revised 9 June 2000, Accepted 14 June 2000, Available online 4 August 2000. The authors would like to thank Pharmacia & Upjohn for use of their 800 MHz spectrometer and Toshi Nishida for assistance. This work was sponsored in part by grants from the Swedish Academy of Sciences (KVA) and Natural Sciences Research Council (NFR) (to TH), the UK MRC and the NIH (to VR), the Russian Academy of Sciences, and the Russian Foundation for Basic research (to MG). MG was supported in part by the International Research Scholar’s award from the Howard Hughes Medical Institute.
Funders:
Funding AgencyGrant Number
Kungliga VetenskapsakademienUNSPECIFIED
Natural Sciences Research CouncilUNSPECIFIED
Medical Research Council (UK)UNSPECIFIED
NIHUNSPECIFIED
Russian Academy of SciencesUNSPECIFIED
Russian Foundation for Basic ResearchUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Subject Keywords:NMR; Ribosomal protein; S16; Thermus thermophilus; Translation; X-ray crystallography
Issue or Number:8
Record Number:CaltechAUTHORS:20181029-110214031
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20181029-110214031
Official Citation:Peter Allard, Alexey V Rak, Brian T Wimberly, William M Clemons, Alexander Kalinin, Magnus Helgstrand, Maria B Garber, V Ramakrishnan, Torleif Härd, Another piece of the ribosome: solution structure of S16 and its location in the 30S subunit, Structure, Volume 8, Issue 8, 2000, Pages 875-882, ISSN 0969-2126, https://doi.org/10.1016/S0969-2126(00)00177-5. (http://www.sciencedirect.com/science/article/pii/S0969212600001775)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:90466
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:29 Oct 2018 18:09
Last Modified:03 Oct 2019 20:25

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