De novo backbone trace of GroEL from single particle electron cryomicroscopy
De novo backbone trace of GroEL from single particle electron cryomicroscopy
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DOI：
10.1016/j.str.2008.02.007
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发表时间：
2008-03-01
期刊：
影响因子：
5.7
通讯作者：
Chiu, Wah
中科院分区：
文献类型：
--
作者：
Ludtke, Steven J.;Baker, Matthew L.;Chiu, Wah
在这项工作中，我们使用单粒子电子冷冻显微镜（cryo-EM）重建了具有D7和C7对称性的类似4埃分辨率的GroEL。利用一种新开发的骨架化算法和二级结构元素识别，结合基于序列的二级结构预测，我们证明了直接从冷冻电镜重建中获得从头C α痕迹是可能的。我们的主干轨迹的拓扑结构是完全准确的，尽管细微的变化表明了与现有晶体结构的显著差异。在C7对称图中，每个环上的7个单体是相同的；然而，亚基在每个环中具有微妙的不同结构，特别是在赤道区域。这些差异包括不对称的盐桥，只有一个环的核苷酸结合袋的密度，以及α螺旋位置的微小变化。这种不对称构象不同于以前的不对称结构，包括GroES-bound GroEL，可能代表伴侣蛋白途径中的“启动状态”。
In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to similar to 4 angstrom resolution with both D7 and C7 symmetry. Using a newly developed skeletonization algorithm and secondary structure element identification in combination with sequence-based secondary structure prediction, we demonstrate that it is possible to achieve a de novo C alpha trace directly from a cryo-EM reconstruction. The topology of our backbone trace is completely accurate, though subtle alterations illustrate significant differences from existing crystal structures. In the map with C7 symmetry, the seven monomers in each ring are identical; however, the subunits have a subtly different structure in each ring, particularly in the equatorial domain. These differences include an asymmetric salt bridge, density in the nucleotide-binding pocket of only one ring, and small shifts in alpha helix positions. This asymmetric conformation is different from previous asymmetric structures, including GroES-bound GroEL, and may represent a "primed state" in the chaperonin pathway.