Refined structure of satellite tobacco mosaic virus at 1.8Å resolution
Refined structure of satellite tobacco mosaic virus at 1.8Å resolution
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DOI：
10.1006/jmbi.1997.1570
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发表时间：
1998-03-20
影响因子：
5.6
通讯作者：
McPherson, A
中科院分区：
文献类型：
--
作者：
Larson, SB;Day, J;McPherson, A
利用从微重力下生长的晶体收集的x射线衍射数据，将卫星烟草花叶病毒（STMV）的分子结构细化到1.8埃分辨率。219086次独立反射的最终X值为0.179，无r值为0.184。不对称单元的最终模型包含一个外壳蛋白单体的13到159个氨基酸残基、21个核苷酸、一个硫酸盐离子和168个水分子。这些核苷酸被可视化为9个碱基对的30个螺旋片段，每个3'端堆叠一个额外的碱基，加上一个“自由”核苷酸，不属于螺旋片段，但与蛋白质紧密结合。硫酸盐离子精确地位于5重轴上，每个都由10个天冬酰胺侧链协调。在10080个结构水（每个不对称单元168个）中，约20%用于在蛋白质-蛋白质和蛋白质-核酸界面上架起大分子成分的桥梁。RNA与蛋白质的结合涉及一些盐键，特别是游离核苷酸的磷酸盐，但主要贡献来自一个复杂的氢键网络。在rna -蛋白界面上有大量的水分子，其中许多充当中间的氢键桥。磷酸糖主链为RNA提供了大部分的供体和受体。螺旋RNA的构象与A型DNA的构象最接近。螺旋段的中心区域最广泛地参与与蛋白质的接触，并且表现出低的热参数，这些参数在末端急剧增加。可见RNA约占病毒粒子中总核酸的59%，来自单链基因组，单链基因组折叠形成螺旋状片段。螺旋和游离核苷酸以连续有效的方式连接，严重限制了剩余的看不见的核酸的处置。利用剩余的核苷酸，可以根据基序折叠RNA，这些基序提供与晶体结构中所见的二十面体对称排列相容的RNA结构元件的周期性分布。在STMV中，蛋白质和核酸之间的密切关系提示了一种基于RNA与衣壳蛋白二聚体协同协调共缩聚的组装途径。(C) 1998学术出版社有限公司
The molecular structure of satellite tobacco mosaic virus (STMV) has been refined to 1.8 Angstrom resolution using X-ray diffraction data collected from crystals grown in microgravity. The final X value was 0.179 and R-free was 0.184 for 219,086 independent reflections. The final model of the asymmetric unit contained amino acid residues 13 to 159 of a coat protein monomer, 21 nucleotides, a sulfate ion, and 168 water molecules. The nucleotides were visualized as 30 helical segments of nine base-pairs with an additional base stacked at each 3' end, plus a "free" nucleotide, not belonging to the helical segments, but firmly bound by the protein. Sulfate ions are located exactly on 5-fold axes and each is coordinated by ten asparagine side-chains. Of the 10,080 structural waters, 168 per asymmetric unit, about 20% serve to bridge the macromolecular components at protein-protein and protein-nucleic acid interfaces. Binding of RNA to the protein involves some salt linkages, particularly to the phosphate of the free nucleotide, but the major contribution is from an intricate network of hydrogen bonds. There are numerous water molecules in the RNA-protein interface, many serving as intermediate hydrogen bond bridges. The sugar-phosphate backbone contributes most of the donors and accepters for the RNA. The helical RNA conformation is nearest that of A form DNA. The central region of a helical segment is most extensively involved in contacts with protein, and exhibits low thermal parameters which increase dramatically toward the ends. The visible RNA represents approximately 59% of the total nucleic acid in the virion and is derived from the single-stranded genome, which has folded upon itself to form helical segments. Linking of the helices and the free nucleotides in a contiguous and efficient manner severely restricts the disposition of the remaining, unseen nucleic acid. Using the remaining nucleotides it is possible to fold the RNA according to motifs that provide a periodic distribution of RNA structural elements compatible with the icosahedrally symmetrical arrangement seen in the crystallographic structure. The intimate relationship between protein and nucleic acid in STMV suggests an assembly pathway based on the cooperative and coordinated co-condensation of RNA with capsid protein dimers. (C) 1998 Academic Press Limited.