RNA 中 K -turn 基序的结构数据库。
A structural database for k-turn motifs in RNA.
机构信息
Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee DD1 5EH, United Kingdom.
出版信息
RNA. 2010 Aug;16(8):1463-8. doi: 10.1261/rna.2207910. Epub 2010 Jun 18.
Abstract
The kink-turn (k-turn) is a common structural motif in RNA that introduces a tight kink into the helical axis. k-turns play an important architectural role in RNA structures and serve as binding sites for a number of proteins. We have created a database of known and postulated k-turn sequences and three-dimensional (3D) structures, available via the internet. This site provides (1) a database of sequence and structure, as a resource for the RNA community, and (2) a tool to enable the manipulation and comparison of 3D structures where known.
摘要
扭结（k-turn）是 RNA 中常见的结构基序，它会使螺旋轴产生强烈的扭曲。k-turn 在 RNA 结构中具有重要的结构作用，并作为许多蛋白质的结合位点。我们已经创建了一个已知和假设的 k-turn 序列和三维（3D）结构数据库，可通过互联网访问。该站点提供了（1）一个序列和结构数据库，作为 RNA 社区的资源，以及（2）一个工具，用于对已知的 3D 结构进行操作和比较。
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本文引用的文献
1
Ion-induced folding of a kink turn that departs from the conventional sequence.
Nucleic Acids Res. 2009 Nov;37(21):7281-9. doi: 10.1093/nar/gkp791.
2
A toolkit for publishing enhanced figures.
J Appl Crystallogr. 2008 Aug 1;41(Pt 4):811-814. doi: 10.1107/S0021889808015616. Epub 2008 Jul 1.
3
Rfam: updates to the RNA families database.
Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40. doi: 10.1093/nar/gkn766. Epub 2008 Oct 25.
4
The importance of G.A hydrogen bonding in the metal ion- and protein-induced folding of a kink turn RNA.
J Mol Biol. 2008 Aug 29;381(2):431-42. doi: 10.1016/j.jmb.2008.05.052. Epub 2008 May 29.
5
Mutations outside the anisomycin-binding site can make ribosomes drug-resistant.
J Mol Biol. 2008 Jun 6;379(3):505-19. doi: 10.1016/j.jmb.2008.03.075. Epub 2008 Apr 8.
6
Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot.
Biochemistry. 2008 Feb 12;47(6):1490-9. doi: 10.1021/bi701164y. Epub 2008 Jan 19.
7
Dynamic interactions within sub-complexes of the H/ACA pseudouridylation guide RNP.
Nucleic Acids Res. 2007;35(18):6196-206. doi: 10.1093/nar/gkm673. Epub 2007 Sep 12.
8
A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control.
RNA. 2007 Aug;13(8):1256-67. doi: 10.1261/rna.560307. Epub 2007 Jun 21.
9
The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA.
RNA. 2007 Feb;13(2):200-10. doi: 10.1261/rna.285707. Epub 2006 Dec 8.
10
Structure of the S-adenosylmethionine riboswitch regulatory mRNA element.
Nature. 2006 Jun 29;441(7097):1172-5. doi: 10.1038/nature04819.
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