Xiong Y, Deng J, Sudarsanakumar C, Sundaralingam M
Department of Chemistry, The Ohio State University Biological Macromolecular Structure Center, 012 Rightmire Hall, 1060 Carmack Rd., Columbus, OH 43210, USA.
J Mol Biol. 2001 Oct 26;313(3):573-82. doi: 10.1006/jmbi.2001.5045.
The crystal structure of a nonamer RNA duplex with a uridine bulge in each strand, r(gugucgcac)(2), was determined at 1.4 A resolution. The structure was solved by multiple anomalous diffraction phasing method using a three-wavelength data set collected at the Advanced Protein Source and refined to a final R(work)/R(free) of 21.2 %/23.4 % with 33,271 independent reflections (Friedel pairs unmerged). The RNA duplex crystallized in the tetragonal space group P4(1)22 with two independent molecules in the asymmetric unit. The unit cell dimensions are a=b=47.18 A and c=80.04 A. The helical region of the nonamer adopts the A-form conformation. The uridine bulges assume similar conformations, with uracils flipping out and protruding into the minor groove. The presence of the bulge induces very large twist angles (approximately +50 degrees) between the base-pairs flanking the bulges while causing profound kinks in the helix axis at the bulges. This severe twist and the large kink in turn produces a very narrow major groove at the middle of the molecule. The ribose sugars of the guanosines before the bulges adopt the C2'-endo conformation while the rest, including the bulges, are in the C3'-endo conformation. The intrastrand phosphate-phosphate (P-P) distance of the phosphate groups flanking the bulges (approximately 4.4 A) are significantly shorter than the average P-P distance in the duplex (6.0 A). This short distance between the two phosphate groups brings the non-bridging oxygen atoms close to each other where a calcium ion is bound to each strand. The calcium ions in molecule 1 are well defined while the calcium ions in molecule 2 are disordered.
测定了每条链都有一个尿苷凸起的九聚体RNA双链体r（gugucgcac）（2）的晶体结构，分辨率为1.4埃。该结构通过多波长异常衍射相位法，利用在先进蛋白质源收集的三波长数据集解析得到，并精修至最终的R（工作）/R（自由）为21.2%/23.4%，有33271个独立反射（未合并弗里德尔对）。该RNA双链体在四方晶系空间群P4（1）22中结晶，不对称单元中有两个独立分子。晶胞参数为a = b = 47.18埃，c = 80.04埃。九聚体的螺旋区域采用A-型构象。尿苷凸起呈现相似的构象，尿嘧啶翻转并突入小沟。凸起的存在导致凸起两侧碱基对之间的扭转角非常大（约+50度），同时在凸起处的螺旋轴上产生明显的扭结。这种严重的扭转和大扭结反过来在分子中部产生了非常狭窄的大沟。凸起之前的鸟苷核糖糖采用C2'-内型构象，而其余部分，包括凸起，处于C3'-内型构象。凸起两侧磷酸基团的链内磷酸-磷酸（P-P）距离（约4.4埃）明显短于双链体中的平均P-P距离（6.0埃）。这两个磷酸基团之间的短距离使非桥连氧原子彼此靠近，钙离子与每条链结合。分子1中的钙离子定义明确，而分子2中的钙离子无序。
