ArticleNucleic acids research2014
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 43 citations in OpenAlex.
- RNAprecis: Prediction of full-detail RNA conformation from the experimentally best-observed sparse parameters.PLoS computational biology · 2026Article
- Derailing the host machinery to achieve replication: how viroid and viroid-like RNAs successfully copy their genomes in hostile territory.RNA biology · 2025Review
- Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15.Proteins · 2023Article
- Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis.Journal of the American Chemical Society · 2023Article
- Article
- Predicting higher-order mutational effects in an RNA enzyme by machine learning of high-throughput experimental data.Frontiers in molecular biosciences · 2022Article
- De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes.Nature methods · 2018Article
- Effects of flanking regions on HDV cotranscriptional folding kinetics.RNA (New York, N.Y.) · 2018Article
- Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.Biochemistry · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- MolProbity: More and better reference data for improved all-atom structure validation.Protein science : a publication of the Protein Society · 2018Article
- 'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response.Nucleic acids research · 2016Article
- Secondary structure confirmation and localization of Mg2+ ions in the mammalian CPEB3 ribozyme.RNA (New York, N.Y.) · 2016Article
- A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.ACS catalysis · 2016Article
- Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.RNA (New York, N.Y.) · 2015Article
- New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.Nucleic acids research · 2015Review
- Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density.Biochemistry · 2015Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.
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