ArticlePloS one2014
Secondary structures of rRNAs from all three domains of life.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
88 citing papers in PubMed.
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- A new contribution to the subclass Cyrtophoria (Protista, Ciliophora): a brief revision of Chilodonellidae, including reports of three species and one new genus.Marine life science & technology · 2026Article
- Distinct steps of nuclear maturation of human pre-60S complexes require the activity of GTPases including GNL3L.Nucleic acids research · 2026Article
- Assessing Species Delimitation inMicroorganisms · 2026Article
- Naphthyridine carbamate dimer ligand induces formation of Z-RNA-like fold of disease-related RNA and exhibits a molecular glue characteristics in crystal lattice formation.Nucleic acids research · 2025Article
- Cryo-EM structure of ribosome from pathogenic protozoa Entamoeba histolytica reveals unique features of its architecture.Nature communications · 2025Article
- ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations.Genome biology · 2025Article
- An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation.Molecular cell · 2025Article
- Characterization and optimization of azo dyes degrading microbes isolated from textile effluent.Scientific reports · 2025Article
- N4-acetylcytidine and other RNA modifications in epitranscriptome: insight into DNA repair and cancer development.Epigenomics · 2025Review
- Semi-supervised segmentation of RNA 3D structures using density-based clustering.Computational and structural biotechnology journal · 2025Article
- Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine.Nature communications · 2024Article
- New insights and investigation: Morphomolecular notes on the infraciliature, taxonomy, and systematics of pleurostomatid ciliates (Protozoa, Ciliophora), with establishment of a new suborder, two new genera, and three new species.Zoological research · 2024Article
- Putting It All Together: The Roles of Ribosomal Proteins in Nucleolar Stages of 60S Ribosomal Assembly in the YeastBiomolecules · 2024Review
- Reduction of Ribosomal Expansion Segments in Yeast Species of the Magnusiomyces/Saprochaete Clade.Genome biology and evolution · 2024Article
- Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN.Nature methods · 2024Article
- The 3 31 Nucleotide Minihelix tRNA Evolution Theorem and the Origin of Life.Life (Basel, Switzerland) · 2023Review
- Ancestry of RNA/RNA interaction regions within segmented ribosomes.RNA (New York, N.Y.) · 2023Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only), Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery). Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision).
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