McKenna R, Ilag L L, Rossmann M G
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907.
J Mol Biol. 1994 Apr 15;237(5):517-43. doi: 10.1006/jmbi.1994.1253.
The structure of the bacteriophage phi X174 was examined in a 2.7 A resolution map and refined, using 6.0 A to 3.0 A resolution data with F > or = 5 sigma (F). The final R-factor was 20.9% and the root-mean-square deviation from idealized bond lengths was 0.021 A. The Hendrickson-Konnert refinement was restrained by the phases derived from the molecular replacement icosahedral averaging procedure. The mature phage capsid consists of 60 copies of the F protein with 426 amino acids, the G protein with 175 amino acids and the J protein with 37 amino acids, as well as 12 copies of the H protein with 328 amino acids. The entire polypeptide chain of the F and G protein, all but the first N-terminal residue of the J protein, and 178 solvent molecules were included in the refinement calculations. The secondary structural features of the F, G and J proteins and their interactions with each other are described. The majority of the protein-protein interactions are between the icosahedral 5-fold related interfaces of the F and of the G proteins. These pentameric units of the F and G proteins form the 9S and 6S assembly intermediates, respectively. The J protein lacks any secondary structure and acts as a linking arm between the icosahedral 5-fold related F proteins. Water molecules were introduced only after phase extension to 2.7 A resolution had been completed. The F protein is associated with lower "thermal" parameters and exhibits greater water order in its environment than the G and J proteins. The largest thermal parameters occur in residues on the viral surface. The solvent contributes to the interactions between the proteins. There is an interface of solvent molecules between the F and the G pentamers which stabilizes the pentameric G protein spikes in a crater centered at each of the icosahedral 5-fold vertices of the F protein capsid. Sequence alignments of the F, G and J amino acid sequences for the homologous bacteriophages G4, alpha 3, phi K and phi X174 with respect to the phi X174 structure demonstrated the conservation of functionally important residues on the viral surface.
利用分辨率为6.0 Å至3.0 Å且F≥5σ(F)的数据，在分辨率为2.7 Å的图谱中对噬菌体φX174的结构进行了检测并进行了优化。最终的R因子为20.9%，与理想键长的均方根偏差为0.021 Å。Hendrickson-Konnert优化受到了源自分子置换二十面体平均程序的相位的限制。成熟的噬菌体衣壳由60个含有426个氨基酸的F蛋白、60个含有175个氨基酸的G蛋白、60个含有37个氨基酸的J蛋白以及12个含有328个氨基酸的H蛋白组成。F蛋白和G蛋白的整个多肽链、J蛋白除首个N端残基外的所有部分以及178个溶剂分子都被纳入了优化计算。描述了F、G和J蛋白的二级结构特征及其相互作用。大多数蛋白质-蛋白质相互作用发生在F蛋白和G蛋白的二十面体5倍相关界面之间。F蛋白和G蛋白的这些五聚体单元分别形成9S和6S组装中间体。J蛋白缺乏任何二级结构，充当二十面体5倍相关F蛋白之间的连接臂。仅在相位扩展至2.7 Å分辨率完成后才引入水分子。F蛋白具有较低的“热”参数，并且在其环境中比G蛋白和J蛋白表现出更高的水有序性。最大的热参数出现在病毒表面的残基上。溶剂有助于蛋白质之间的相互作用。在F五聚体和G五聚体之间存在溶剂分子界面，该界面在以F蛋白衣壳的每个二十面体5倍顶点为中心的坑中稳定五聚体G蛋白刺突。针对φX174结构，对同源噬菌体G4、α3、φK和φX174的F、G和J氨基酸序列进行序列比对，结果表明病毒表面功能重要残基具有保守性。
