ArticlePloS one2015
Conjoined use of EM and NMR in RNA structure refinement.
Article in PloS one, 2015. 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, 29 citations in OpenAlex.
- Xplor-NIH: Better parameters and protocols for NMR protein structure determination.Protein science : a publication of the Protein Society · 2024Article
- RNA structure determination: From 2D to 3D.Fundamental research · 2023Review
- Magic-angle-spinning NMR structure of the kinesin-1 motor domain assembled with microtubules reveals the elusive neck linker orientation.Nature communications · 2022Article
- Visualization of Sparsely-populated Lower-order Oligomeric States of Human Mitochondrial Hsp60 by Cryo-electron Microscopy.Journal of molecular biology · 2021Article
- Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy.Wiley interdisciplinary reviews. RNA · 2019Review
- Review
- A pipeline for computational design of novel RNA-like topologies.Nucleic acids research · 2018Article
- Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.Structure (London, England : 1993) · 2018Article
- Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM.Acta crystallographica. Section D, Structural biology · 2018Review
- Protein Structure Elucidation from NMR Data with the Program Xplor-NIH.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Xplor-NIH for molecular structure determination from NMR and other data sources.Protein science : a publication of the Protein Society · 2018Article
- CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.The journal of physical chemistry. B · 2017Article
- In situ high-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum.Nature communications · 2016Article
- Structure of the Dimerization Interface in the Mature HIV-1 Capsid Protein Lattice from Solid State NMR of Tubular Assemblies.Journal of the American Chemical Society · 2016Article
- Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA.Journal of molecular biology · 2016Article
- Article
- Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.Structure (London, England : 1993) · 2015Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
More than 40% of the RNA structures have been determined using nuclear magnetic resonance (NMR) technique. NMR mainly provides local structural information of protons and works most effectively on relatively small biomacromolecules. Hence structural characterization of large RNAs can be difficult for NMR alone. Electron microscopy (EM) provides global shape information of macromolecules at nanometer resolution, which should be complementary to NMR for RNA structure determination. Here we developed a new energy term in Xplor-NIH against the density map obtained by EM. We conjointly used NMR and map restraints for the structure refinement of three RNA systems—U2/U6 small-nuclear RNA, genome-packing motif (Ψ(CD))2 from Moloney murine leukemia virus, and ribosome-binding element from turnip crinkle virus. In all three systems, we showed that the incorporation of a map restraint, either experimental or generated from known PDB structure, greatly improves structural precision and accuracy. Importantly, our method does not rely on an initial model assembled from RNA duplexes, and allows full torsional freedom for each nucleotide in the torsion angle simulated annealing refinement. As increasing number of macromolecules can be characterized by both NMR and EM, the marriage between the two techniques would enable better characterization of RNA three-dimensional structures.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.