A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 A.
A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 A.
复制标题
大肠杆菌 16S 核糖体 RNA 三维折叠的新模型。
DOI：
--
复制
发表时间：
1997
影响因子：
5.6
通讯作者：
R. Brimacombe
中科院分区：
文献类型：
--
作者：
F. Mueller;R. Brimacombe
最近发表的模型大肠杆菌70 S核糖体在20 A的分辨率，通过冷冻电子显微镜（cryo-EM）结合计算机图像处理技术，表现出两个功能，直接相关的rRNA分子的原位三维折叠。首先，在这个分辨率水平上，许多精细的结构细节是可见的，其中一些具有与核酸螺旋的尺寸相当的尺寸。其次，在前和后易位状态的核糖体的重建中，可以看到密度分别直接对应于A和P位点tRNA，以及P和E位点tRNA，从而使30 S亚基上的解码区能够相当精确地定位。因此，我们已经完善了我们以前的模型为16 S rRNA，生化证据的基础上，通过拟合它的cryo-EM轮廓的核糖体携带A和P位点的tRNA。为此，最直接相关的证据包括解码区中新的定点交联数据，其定义了16 S rRNA和mRNA之间或16 S rRNA和tRNA之间在A、P和E位点的接触集;这些接触位点可以直接与EM结构中的tRNA位置相关。该模型扩展到其他部分的16 S分子，通过拟合的16 S rRNA的良好建立的二级结构的各个元素到适当的精细结构元素的EM轮廓，在同一时间考虑到其他数据中使用的先前的模型，如内RNA交联内的16 S rRNA本身。在模型中还考虑了大量可用的RNA-蛋白质交联和足迹数据，以便将rRNA折叠与通过中子散射和免疫电子显微镜测定的30 S核糖体蛋白的已知分布相关联。绝大多数生化数据点涉及rRNA的单链区域，因此，与大多数以前的模型相比，在专门开发的建模程序ERNA-3D的帮助下，单链区域被包括在我们的结构中。这使得各种生物化学数据集可以直接显示在本文和随附论文中，在cryo-EM轮廓内rRNA结构的适当部分的图表上。
Recently published models of the Escherichia coli 70 S ribosome at 20 A resolution, obtained by cryo-electron microscopy (cryo-EM) combined with computerized image processing techniques, exhibit two features that are directly relevant to the in situ three-dimensional folding of the rRNA molecules. First, at this level of resolution many fine structural details are visible, a number of them having dimensions comparable to those of nucleic acid helices. Second, in reconstructions of ribosomes in the pre- and post-translocational states, density can be seen that corresponds directly to the A and P site tRNAs, and to the P and E site tRNAs, respectively, thus enabling the decoding region on the 30 S subunit to be located rather precisely. Accordingly, we have refined our previous model for the 16 S rRNA, based on biochemical evidence, by fitting it to the cryo-EM contour of ribosomes carrying A and P site tRNAs. For this purpose, the most immediately relevant evidence consists of new site-directed cross-linking data in the decoding region, which define sets of contacts between the 16 S rRNA and mRNA, or between 16 S rRNA and tRNA at the A, P and E sites; these contact sites can be correlated directly with the tRNA positions in the EM structure. The model is extended to other parts of the 16 S molecule by fitting individual elements of the well-established secondary structure of the 16 S rRNA into the appropriate fine structural elements of the EM contour, at the same time taking into account other data used in the previous model, such as intra-RNA cross-links within the 16 S rRNA itself. The large body of available RNA-protein cross-linking and foot-printing data is also considered in the model, in order to correlate the rRNA folding with the known distribution of the 30 S ribosomal proteins as determined by neutron scattering and immuno-electron microscopy. The great majority of the biochemical data points involve single-stranded regions of the rRNA, and therefore, in contrast to most previous models, the single-stranded regions are included in our structure, with the help of a specially developed modelling programme, ERNA-3D. This allows the various biochemical data sets to be displayed directly, in this and in the accompanying papers, on diagrams of appropriate parts of the rRNA structure within the cryo-EM contour.
登录
查看更多内容
基于化学足迹数据定义 16S rRNA 允许构象空间的计算方法。
DOI：
--
发表时间：
1996
期刊：
RNA (New York, N.Y.)
影响因子：
--
作者：
Fink,DL;Chen,RO;Noller,HF;Altman,RB
通讯作者：
Altman,RB
影响因子：
5.6
作者：
MOAZED, D;STERN, S;NOLLER, HF
通讯作者：
NOLLER, HF
DOI：
--
发表时间：
1982
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Trempe,MR;Ohgi,K;Glitz,DG
通讯作者：
Glitz,DG
遗传和比较分析揭示了大肠杆菌 16S rRNA nt 912 区域的替代二级结构。
DOI：
10.1073/pnas.92.23.10555
发表时间：
1995
影响因子：
11.1
作者：
Lodmell,JS;Gutell,RR;Dahlberg,AE
通讯作者：
Dahlberg,AE
16 S 核糖体 RNA 三维折叠模型。
影响因子：
5.6
作者：
Stern,S;Weiser,B;Noller,HF
通讯作者：
Noller,HF