Analysis of the single-stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A.
Analysis of the single-stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A.
复制标题
单链 DNA 噬菌体 phi X174 的分析，分辨率为 3.0 A。
DOI：
--
复制
发表时间：
1994
影响因子：
5.6
通讯作者：
Michael G. Rossmann
中科院分区：
文献类型：
--
作者：
Robert McKenna;L. Ilag;Michael G. Rossmann
在2.7 A分辨率图中检查噬菌体phi X174的结构，并使用6.0 A至3.0 A分辨率数据进行细化，其中F >或= 5 σ（F）。最终R因子为20.9%，与理想键长的均方根偏差为0.021 A。Hendrickson-Konnert细化受到来自分子置换二十面体平均程序的相的限制。成熟的噬菌体衣壳由60个拷贝的具有426个氨基酸的F蛋白、具有175个氨基酸的G蛋白和具有37个氨基酸的J蛋白以及12个拷贝的具有328个氨基酸的H蛋白组成。F和G蛋白的整个多肽链、J蛋白的第一个N-末端残基以外的所有残基以及178个溶剂分子都包括在精细计算中。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-蛋白质相互作用是F蛋白和G蛋白的二十面体5重相关界面之间的。F和G蛋白的这些五聚体单元分别形成9 S和6S组装中间体。J蛋白缺乏任何二级结构，并作为二十面体5倍相关F蛋白之间的连接臂。仅在完成相延伸至2.7 A分辨率后才引入水分子。F蛋白与较低的“热”参数，并表现出更大的水秩序在其环境中比G和J蛋白。最大的热参数发生在病毒表面上的残留物中。溶剂有助于蛋白质之间的相互作用。在F和G五聚体之间存在溶剂分子的界面，其使五聚体G蛋白尖峰稳定在以F蛋白衣壳的二十面体5重顶点中的每一个为中心的凹坑中。同源噬菌体G4、α 3、phi K和phi X174的F、G和J氨基酸序列相对于phi X174结构的序列比对证明了病毒表面上功能重要残基的保守性。
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.