X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr(2+) ions at subatomic resolution (0.61 Å)

Four-stranded guanine tetraplexes in RNA have been identified to be involved in crucial biological functions, such as dimerization of retroviral RNA, translational repression, and mRNA turnover. However, the structural basis for these biological processes is still largely unknown. Here we report the RNA tetraplex structure (UGGGGU)(4) at ultra-high resolution (0.61 Å). The space group is P42(1)2, and cell constants are a = b = 36.16 Å and c = 74.09 Å. The structure was solved by the multiple-wavelength anomalous dispersion method using a set of three-wavelength data of the isomorphous bromo derivative (br)UGGGGU and refined to 0.61-Å resolution. Each of the four strands in the asymmetric unit forms a parallel tetraplex with symmetry-related molecules. The tetraplex molecules stack on one another in opposite polarity (head-to-head or tail-to-tail) to form a pseudocontinuous column. All of the 5′-end uridines rotate around the backbone of G2, swing out, and form unique octaplexes with the neighboring G tetraplexes, whereas the 3′-end uridines are stacked-in and form uridine tetrads. All of the bases are anti, and the riboses are in the mixed C2′- and C3′-puckering mode. Strontium ions are observed in every other guanine tetrad plane, sitting on the fourfold axis and associated to the eight O6 atoms of neighboring guanine bases in a bipyramidal-antiprism geometry. The hydrogens are clearly observed in the structure.

RNA中的四链鸟嘌呤四联体（four-stranded guanine tetraplexes）已被证实参与诸多关键生物学功能，例如逆转录病毒RNA的二聚化、翻译抑制以及mRNA周转调控。然而，这些生物学过程背后的结构基础仍未被充分阐明。本研究报道了分辨率达0.61埃的RNA四联体结构(UGGGGU)₄。该晶体的空间群（space group）为P42₁2，晶胞参数（cell constants）为a = b = 36.16 Å，c = 74.09 Å。本结构通过多波长反常散射法（multiple-wavelength anomalous dispersion method）解析，所用数据采集自同晶型溴代衍生物(br)UGGGGU的三组波长衍射数据集，并最终精修至0.61埃分辨率。不对称单元（asymmetric unit）内的四条单链分别与对称相关的分子形成平行四联体结构。各四联体分子以相反极性（头对头或尾对尾）相互堆叠，形成伪连续柱状结构。所有5'端尿苷均围绕G2的骨架旋转并向外伸出，与邻近的鸟嘌呤四联体形成独特的八联体结构；而3'端尿苷则嵌入堆叠，形成尿苷四联体。所有碱基均处于反式构象，核糖环则采取C2'和C3'混合的糖环折叠模式。每隔一层鸟嘌呤四联体平面即可观测到锶离子：这些离子位于四重轴上，以双锥反棱柱几何构型与邻近鸟嘌呤碱基的8个O6原子相结合。本结构中可清晰观测到氢原子。