Local defocus estimation in single particle analysis in cryo-electron microscopy

IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
E. Fernandez-Gimenez , J.M. Carazo , C.O.S. Sorzano
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引用次数: 0

Abstract

Single Particle analysis (SPA) aims to determine the three-dimensional structure of proteins and macromolecular complexes. The current state of the art has allowed us to achieve near-atomic and even atomic resolutions. To obtain high-resolution structures, a set of well-defined image processing steps is required. A critical one is the estimation of the Contrast Transfer Function (CTF), which considers the sample defocus and aberrations of the microscope. Defocus is usually globally estimated; in this case, it is the same for all the particles in each micrograph. But proteins are ice-embedded at different heights, suggesting that defocus should be measured in a local (per particle) manner. There are four state-of-the-art programs to estimate local defocus (Gctf, Relion, CryoSPARC, and Xmipp). In this work, we have compared the results of these software packages to check whether the resolution improves. We have used the Scipion framework and developed a specific program to analyze local defocus. The results produced by different programs do not show a clear consensus using the current test datasets in this study.

Abstract Image

冷冻电子显微镜中单粒子分析中的局部散焦估计。
单粒子分析(SPA)旨在确定蛋白质和大分子复合物的三维结构。当前的技术状态使我们能够实现接近原子甚至原子的分辨率。为了获得高分辨率的结构,需要一组定义明确的图像处理步骤。一个关键的问题是对比度传递函数(CTF)的估计,它考虑了样品的散焦和显微镜的像差。散焦通常是全局估计的;在这种情况下,每个显微照片中的所有粒子都是相同的。但蛋白质是嵌在不同高度的冰,这表明散焦应该以局部(每个颗粒)的方式进行测量。有四个最先进的程序来估计局部散焦(Gctf、Relion、CryoSPARC和Xmipp)。在这项工作中,我们比较了这些软件包的结果,以检查分辨率是否有所提高。我们使用了Scipion框架,并开发了一个特定的程序来分析局部散焦。使用本研究中当前的测试数据集,不同程序产生的结果没有显示出明确的共识。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of structural biology
Journal of structural biology 生物-生化与分子生物学
CiteScore
6.30
自引率
3.30%
发文量
88
审稿时长
65 days
期刊介绍: Journal of Structural Biology (JSB) has an open access mirror journal, the Journal of Structural Biology: X (JSBX), sharing the same aims and scope, editorial team, submission system and rigorous peer review. Since both journals share the same editorial system, you may submit your manuscript via either journal homepage. You will be prompted during submission (and revision) to choose in which to publish your article. The editors and reviewers are not aware of the choice you made until the article has been published online. JSB and JSBX publish papers dealing with the structural analysis of living material at every level of organization by all methods that lead to an understanding of biological function in terms of molecular and supermolecular structure. Techniques covered include: • Light microscopy including confocal microscopy • All types of electron microscopy • X-ray diffraction • Nuclear magnetic resonance • Scanning force microscopy, scanning probe microscopy, and tunneling microscopy • Digital image processing • Computational insights into structure
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