ArticleRNA (New York, N.Y.)2014
Principles of ion recognition in RNA: insights from the group II intron structures.
Article in RNA (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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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
27 citing papers in PubMed, 51 citations in OpenAlex.
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- Controlled dynamic remodeling of the spliceosome active site enables the first step of splicing.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.Proteins · 2026Article
- Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.Nature communications · 2025Article
- The structure, folding kinetics, and dynamics of long poly(UG) RNA.Nucleic acids research · 2025Article
- Structural basis of circularly permuted group II intron self-splicing.Nature structural & molecular biology · 2025Article
- Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers.bioRxiv : the preprint server for biology · 2025Article
- Targeting RNA with small molecules, from RNA structures to precision medicines: IUPHAR review: 40.British journal of pharmacology · 2024Review
- Targeting the conserved active site of splicing machines with specific and selective small molecule modulators.Nature communications · 2024Article
- Finding the Ion in the RNA-Stack: Can Computational Models Accurately Predict Key Functional Elements in Large Macromolecular Complexes?Journal of chemical information and modeling · 2021Article
- Structural Insights Into the 5'UG/3'GU Wobble Tandem in Complex With BaFrontiers in molecular biosciences · 2021Article
- Age-Specific Modulation of Prefrontal Cortex LTP by Glucocorticoid Receptors Following Brief Exposure to HFD.Frontiers in synaptic neuroscience · 2021Article
- Unraveling the structure and biological functions of RNA triple helices.Wiley interdisciplinary reviews. RNA · 2020Review
- Visualizing group II intron dynamics between the first and second steps of splicing.Nature communications · 2020Article
- Visualizing the functional 3D shape and topography of long noncoding RNAs by single-particle atomic force microscopy and in-solution hydrodynamic techniques.Nature protocols · 2020Article
- Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts.Nature communications · 2020Article
- Nucleobase carbonyl groups are poor MgRNA (New York, N.Y.) · 2019Article
- Optimal molecular crowding accelerates group II intron folding and maximizes catalysis.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes.Structure (London, England : 1993) · 2018Article
- Structural Insights into the Mechanism of Group II Intron Splicing.Trends in biochemical sciences · 2017Review
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Metal ions promote both RNA folding and catalysis, thus being essential in stabilizing the structure and determining the function of large RNA molecules, including group II introns. The latter are self-splicing metalloribozymes, containing a heteronuclear four-metal-ion center within the active site. In addition to these catalytic ions, group II introns bind many other structural ions, including delocalized ions that bind the RNA diffusively and well-ordered ions that bind the RNA tightly with high occupancy. The latter ions, which can be studied by biophysical methods, have not yet been analyzed systematically. Here, we compare crystal structures of the group IIC intron from Oceanobacillus iheyensis and classify numerous site-bound ions, which are primarily localized in the intron core and near long-range tertiary contacts. Certain ion-binding sites resemble motifs observed in known RNA structures, while others are idiosyncratic to the group II intron. Particularly interesting are (1) ions proximal to the active site, which may participate in splicing together with the catalytic four-metal-ion center, (2) organic ions that bind regions predicted to interact with intron-encoded proteins, and (3) unusual monovalent ions bound to GU wobble pairs, GA mismatches, the S-turn, the tetraloop-receptor, and the T-loop. Our analysis extends the general principles by which ions participate in RNA structural organization and it will aid in the determination and interpretation of future RNA structures.
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