title: Conjoined use of EM and NMR in RNA structure refinement.
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.
authors: CAS Key Laboratory of Magnetic Resonance in Biological Systems, National Magnetic Resonance Center at Wuhan, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China.
authors: Zhou
authors: Z
authors: Gong
authors: Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, MD 20892, United States of America.
authors: Charles D
authors: CD
authors: Schwieters
authors: CAS Key Laboratory of Magnetic Resonance in Biological Systems, National Magnetic Resonance Center at Wuhan, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China.
authors: Chun
authors: C
authors: Tang
mesh_terms: D016679:Genome, Viral / Q000235:genetics; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008854:Microscopy, Electron / Q000379:methods*; D008958:Models, Molecular; D008979:Moloney murine leukemia virus / Q000235:genetics; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA