The accuracy of ribosomal RNA comparative structure models
Abstract
The determination of the 16S and 23S rRNA secondary structure models was initiated shortly after the first complete 16S and 23S rRNA sequences were determined in the late 1970s. The structures that are common to all 16S rRNAs and all 23S rRNAs were determined using comparative methods from the analysis of thousands of rRNA sequences. Twenty-plus years later, the 16S and 23S rRNA comparative structure models have been evaluated against the recently determined high-resolution crystal structures of the 30S and 50S ribosomal subunits. Nearly all of the predicted covariation-based base pairs, including the regular base pairs and helices, and the irregular base pairs and tertiary interactions, were present in the 30S and 50S crystal structures.
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The BLS alignment contains about 99% of bacterial sequences.
“Given that the BLS alignment contains about 99% of bacterial sequences, it is possible to map its columns to the bases of the state-of-the-art structural model of the 16S bacterial rRNA defined on the Comparative RNA Web43.”
From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [43]
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In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
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Improving microbial phylogeny with citizen science within a mass-market video game
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- Authors
- Gutell, R. R., Lee, J. C., & Cannone, J. J.
- Affiliations
- The University of Texas at Austin (US)
- Corresponding author
- Gutell, Robin R
- Venue
- Current Opinion in Structural Biology
- Publisher
- Elsevier BV
- Published
- 2002-06
- Volume
- 12
- Issue
- 3
- Pages
- 301-310
- ISSN
- 0959-440X (ISSN-L)
- OpenAlex
- W2159548583
- Cited by
- 364
- References
- 2
- Citations by year
- 2026: 2 · 2025: 11 · 2024: 9 · 2023: 11 · 2022: 12 · 2021: 10 · 2020: 8 · 2019: 9 · 2018: 12 · 2017: 13 · 2016: 16 · 2015: 17 · 2014: 21 · 2013: 22 · 2012: 19
- FWCI
- 1.28
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Current Opinion in Structural Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- University of Texas at Austin
- National Institutes of Health
- National Institute of General Medical Sciences (GM48207, R01GM048207)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Keywords
- 16S rRNA, 23S rRNA, ribosomal RNA secondary structure, 30S ribosomal subunit, 50S ribosomal subunit, crystal structure validation, tertiary interactions, ribosome
- MeSH terms
- Models, Molecular, RNA, Ribosomal, Genetic Variation, Crystallography, X-Ray
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