一种含有钩形转角的26个核苷酸的RNA的晶体结构。
The crystal structure of a 26-nucleotide RNA containing a hook-turn.
作者信息
Szép Szilvia, Wang Jimin, Moore Peter B
机构信息
Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
出版信息
RNA. 2003 Jan;9(1):44-51. doi: 10.1261/rna.2107303.
Abstract
A crystal structure has been obtained for a 26-nucleotide RNA that contains the loop E sequence from Chromatium minutissimum. Rather than having a loop E-like conformation, it consists of an A-form helix that splits into two separate strands following a sheared A-G base pair. The backbone of the strand containing the G of the A-G pair makes a turn of almost 180 degrees in the space of two nucleotides, and then interacts with the minor groove of the helix from which it originates. Similar structures, which we call hook-turns, occur in 16S and 23S rRNAs. They are found at places where the two strands of a helix separate at an A/G juxtaposition to interact with other sequences.
摘要
已获得一种含有微小色菌环E序列的26个核苷酸的RNA的晶体结构。它并非具有类似环E的构象，而是由一个A-型螺旋组成，该螺旋在一个剪切的A-G碱基对后分裂成两条单独的链。包含A-G对中G的链的主链在两个核苷酸的空间内旋转近180度，然后与它起源的螺旋的小沟相互作用。类似的结构，我们称之为钩形转角，出现在16S和23S rRNA中。它们出现在螺旋的两条链在A/G并列处分开以与其他序列相互作用的地方。
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本文引用的文献
1
Processing of X-ray diffraction data collected in oscillation mode.振荡模式下收集的X射线衍射数据的处理。
Methods Enzymol. 1997;276:307-26. doi: 10.1016/S0076-6879(97)76066-X.
2
The CCP4 suite: programs for protein crystallography.CCP4软件包：用于蛋白质晶体学的程序。
Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3. doi: 10.1107/S0907444994003112.
3
The non-Watson-Crick base pairs and their associated isostericity matrices.非沃森-克里克碱基对及其相关的等排性矩阵。
Nucleic Acids Res. 2002 Aug 15;30(16):3497-531. doi: 10.1093/nar/gkf481.
4
High resolution structure of the large ribosomal subunit from a mesophilic eubacterium.来自嗜温真细菌的大核糖体亚基的高分辨率结构。
Cell. 2001 Nov 30;107(5):679-88. doi: 10.1016/s0092-8674(01)00546-3.
5
Implementation of molecular replacement in AMoRe.在AMoRe中分子置换的实施。
Acta Crystallogr D Biol Crystallogr. 2001 Oct;57(Pt 10):1367-72. doi: 10.1107/s0907444901012422. Epub 2001 Sep 21.
6
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EMBO J. 2001 Aug 1;20(15):4214-21. doi: 10.1093/emboj/20.15.4214.
7
RNA tertiary interactions in the large ribosomal subunit: the A-minor motif.大核糖体亚基中的RNA三级相互作用：A- minor基序
Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):4899-903. doi: 10.1073/pnas.081082398. Epub 2001 Apr 10.
8
Structure of the 30S ribosomal subunit.30S核糖体亚基的结构。
Nature. 2000 Sep 21;407(6802):327-39. doi: 10.1038/35030006.
9
Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution.功能激活的小核糖体亚基在3.3埃分辨率下的结构。
Cell. 2000 Sep 1;102(5):615-23. doi: 10.1016/s0092-8674(00)00084-2.
10
Structural motifs in RNA.RNA中的结构基序。
Annu Rev Biochem. 1999;68:287-300. doi: 10.1146/annurev.biochem.68.1.287.
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