ArticleRNA (New York, N.Y.)2000
Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge.
Article in RNA (New York, N.Y.), 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
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- A Bayes-inspired theory for optimally building an efficient coarse-grained folding force field.Communications in information and systems · 2021Article
- FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds.Structure (London, England : 1993) · 2020Article
- Characterization of a novel association between two trypanosome-specific proteins and 5S rRNA.PloS one · 2012Article
- Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.Journal of computational chemistry · 2011Article
- Coarse-grained model for simulation of RNA three-dimensional structures.The journal of physical chemistry. B · 2010Article
- Base-tetrad swapping results in dimerization of RNA quadruplexes: implications for formation of the i-motif RNA octaplex.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae.Molecular genetics and genomics : MGG · 2005Article
- 5S rRNA: Structure and Function from Head to Toe.International journal of biomedical science : IJBS · 2005Article
- 5S rRNA: Structure and Function from Head to Toe.International journal of biomedical science : IJBS · 2005Article
- 5 S rRNA: structure and interactions.The Biochemical journal · 2003Review
- 5S Ribosomal RNA Database.Nucleic acids research · 2002Article
- Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple.RNA (New York, N.Y.) · 2001Article
- X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid.RNA (New York, N.Y.) · 2001Article
- Eukaryotic 5S rRNA biogenesis.Wiley interdisciplinary reviews. RNAReview
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2 authors.
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Abstract
The crystal structure of r(GCCACCCUG).r(CAGGGUCGGC), helix II of the Xenopus laevis 5S rRNA with a cytosine bulge (underlined), has been determined in two forms at 2.2 A (Form I, space group P4(2)2(1)2, a = b = 57.15 A and c = 43.54 A) and 1.7 A (Form II, space group P4(3)2(1)2, a = b = 32.78 A and c = 102.5 A). The helical regions of the nonamers are found in the standard A-RNA conformations and the two forms have an RMS deviation of 0.75 A. However, the cytosine bulge adopts two significantly different conformations with an RMS deviation of 3.9 A. In Form I, the cytosine bulge forms an intermolecular C+*G.C triple in the major groove of a symmetry-related duplex with intermolecular hydrogen bonds between N4C and O6G, and between protonated N3+C and N7G. In contrast, a minor groove C*G.C triple is formed in Form II with intermolecular hydrogen bonds between O2C and N2G, and between N3C and N3G with a water bridge. A partial major groove opening was observed in Form I structure at the bulge site. Two Ca2+ ions were found in Form I helix whereas there were none in Form II. The structural comparison of these two forms indicates that bulged residues can adopt a variety of conformations with little perturbation to the global helix structure. This suggests that bulged residues could function as flexible latches in bridging double helical motifs and facilitate the folding of large RNA molecules.
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