Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
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DOI：
10.7554/elife.17219
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发表时间：
2016-09-26
期刊：
影响因子：
7.7
通讯作者：
DiMaio, Frank
中科院分区：
文献类型：
--
作者：
Wang, Ray Yu-Ruei;Song, Yifan;DiMaio, Frank
Cryo-EM以近原子分辨率（3 - 4.5埃）揭示了许多具有挑战性但令人兴奋的大分子组装体的结构，为生物现象提供了分子描述。然而，在这些分辨率下，精确定位单个原子仍然具有挑战性且容易出错。人工精制数千种氨基酸--在大分子组装中很常见--是一件繁琐而耗时的工作。我们提出了一种自动化的方法，可以提高原子的细节模型，手动建立在近原子分辨率的冷冻-EM地图。将该方法应用于最近通过冷冻EM解决的三个系统，我们能够在保持拟合密度的同时改善模型几何形状。主干放置错误自动检测和纠正，和细化显示了大半径的收敛。结果表明，该方法适用于具有对称性的结构，非常大的尺寸，并含有RNA以及共价结合的配体。该方法应简化冷冻EM结构测定过程，提供准确和公正的原子结构的解释，这样的地图。
Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5 angstrom), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.