The continual improvement of methods for RNA 3D structure modeling and prediction requires accurate and statistically meaningful data concerning RNA structure, both for extraction of knowledge and for benchmarking of structure predictions. The source of sufficiently accurate structural data for these purposes is atomic-resolution X-ray structures of RNA nucleotides, oligonucleotides, and biologically functional RNA molecules. All of our basic knowledge of bond lengths, angles, and stereochemistry in RNA nucleotides, as well as their interaction preferences, including all types of base-pairing, base-stacking, and base-backbone interactions, is ultimately extracted from X-ray structures. One key requirement for reference databases intended for knowledge extraction is the nonredundancy of the structures that are included in the analysis, to avoid bias in the deduced frequency parameters. Here, we address this issue and detail how we produce, on a largely automated and ongoing basis, nonredundant lists of atomic-resolution structures at different resolution thresholds for use in knowledge-driven RNA applications. The file collections are available for download at http://rna.bgsu.edu/nrlist. The primary lists that we provide only include X-ray structures, organized by resolution thresholds, but for completeness, we also provide separate lists that include structures solved by NMR or cryo-EM.
Equivalence Class Asymmetric Unit Longe Chain Hairpin Loop Hammerhead Ribozyme
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in to check access
We thank Eric Westhof for encouragement and guidance in writing this chapter and Anton Petrov for the help with editing and figures.
Funding. National Institutes of Health (Grant No. 1R01GM085328-01A1 to C.L.Z. and N.B.L.).
Cate JH, Gooding AR et al (1996) Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273(5282):1678–1685PubMedCrossRefGoogle Scholar
Chi YI, Martick M et al (2008) Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PLoS Biol 6(9):e234PubMedCrossRefGoogle Scholar
Correll CC, Munishkin A et al (1998) Crystal structure of the ribosomal RNA domain essential for binding elongation factors. Proc Natl Acad Sci USA 95(23):13436–13441PubMedCrossRefGoogle Scholar
Correll CC, Beneken J et al (2003) The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure. Nucleic Acids Res 31(23):6806–6818PubMedCrossRefGoogle Scholar
Garst AD, Heroux A et al (2008) Crystal structure of the lysine riboswitch regulatory mRNA element. J Biol Chem 283(33):22347–22351PubMedCrossRefGoogle Scholar
Kiliszek A, Kierzek R et al (2010) Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases. Nucleic Acids Res 38(22):8370–6Google Scholar
Korostelev A, Asahara H et al (2008) Crystal structure of a translation termination complex formed with release factor RF2. Proc Natl Acad Sci USA 105(50):19684–19689PubMedCrossRefGoogle Scholar
Kulshina N, Baird NJ et al (2009) Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nat Struct Mol Biol 16(12):1212–1217PubMedCrossRefGoogle Scholar
Nussinov R, Jacobson AB (1980) Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci USA 77(11):6309–6313PubMedCrossRefGoogle Scholar
Nussinov R, Pieczenik G et al (1978) Algorithms for loop matchings. SIAM J Appl Math 35(1):68–82CrossRefGoogle Scholar
Oubridge C, Ito N et al (1994) Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 372(6505):432–8Google Scholar
Oubridge C, Ito N et al (1995) Crystallisation of RNA-protein complexes. II. The application of protein engineering for crystallisation of the U1A protein-RNA complex. J Mol Biol 249(2):409–23Google Scholar
Petrov AI, Zirbel CL et al (2011) WebFR3D – a server for finding, aligning and analyzing recurrent RNA 3D motifs. Nucleic Acids Res 39:W50–W55PubMedCrossRefGoogle Scholar
Rahrig RR, Leontis NB et al (2010) R3D Align: global pairwise alignment of RNA 3D structures using local superpositions. Bioinformatics 26(21):2689–2697PubMedCrossRefGoogle Scholar
Reiter NJ, Osterman A et al (2010) Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature 468(7325):784–789PubMedCrossRefGoogle Scholar
Richardson JS, Schneider B et al (2008) RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA 14(3):465–481PubMedCrossRefGoogle Scholar
Sarver M, Zirbel CL et al (2008) FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol 56(1–2):215–252PubMedGoogle Scholar
Schmeing TM, Voorhees RM et al (2009) The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science 326(5953):688–694PubMedCrossRefGoogle Scholar
Selmer M, Dunham CM et al (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313(5795):1935–1942PubMedCrossRefGoogle Scholar
Serganov A, Huang L et al (2008) Structural insights into amino acid binding and gene control by a lysine riboswitch. Nature 455(7217):1263–1267PubMedCrossRefGoogle Scholar
Smith KD, Lipchock SV et al (2009) Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol 16(12):1218–1223PubMedCrossRefGoogle Scholar
Smith KD, Lipchock SV et al (2010) Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch. Biochemistry 49(34):7351–7359PubMedCrossRefGoogle Scholar
Zhu J, Korostelev A et al (2011) Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome. Proc Natl Acad Sci USA 108(5):1839–1844PubMedCrossRefGoogle Scholar