Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis,Journal of Chemical Information and Modeling

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Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2018-05-21 00:00:00 , DOI: 10.1021/acs.jcim.8b00149
Yu-Jiao Yang ₁ , Shuai Wang ₁ , Biao Zhang ₁ , Hong-Bin Shen ₁

Affiliation

As a relatively new technology to solve the three-dimensional (3D) structure of a protein or protein complex, single-particle reconstruction (SPR) of cryogenic electron microscopy (cryo-EM) images shows much superiority and is in a rapidly developing stage. Resolution measurement in SPR, which evaluates the quality of a reconstructed 3D density map, plays a critical role in promoting methodology development of SPR and structural biology. Because there is no benchmark map in the generation of a new structure, how to realize the resolution estimation of a new map is still an open problem. Existing approaches try to generate a hypothetical benchmark map by reconstructing two 3D models from two halves of the original 2D images for cross-reference, which may result in a premature estimation with a half-data model. In this paper, we report a new self-reference-based resolution estimation protocol, called SRes, that requires only a single reconstructed 3D map. The core idea of SRes is to perform a multiscale spectral analysis (MSSA) on the map through multiple size-variable masks segmenting the map. The MSSA-derived multiscale spectral signal-to-noise ratios (mSSNRs) reveal that their corresponding estimated resolutions will show a cliff jump phenomenon, indicating a significant change in the SSNR properties. The critical point on the cliff borderline is demonstrated to be the right estimator for the resolution of the map.

中文翻译：

利用多尺度光谱分析从单个重构的Cryo-EM密度图进行分辨率测量

作为解决蛋白质或蛋白质复合物的三维（3D）结构的相对较新的技术，低温电子显微镜（cryo-EM）图像的单粒子重建（SPR）显示出很多优势，并且处于快速发展阶段。SPR中的分辨率测量可评估重建的3D密度图的质量，在促进SPR和结构生物学的方法学发展中起着至关重要的作用。由于在生成新结构时没有基准图，因此如何实现新图的分辨率估计仍然是一个悬而未决的问题。现有方法试图通过从原始2D图像的两半中重建两个3D模型以进行交叉引用来生成假设的基准图，这可能会导致使用半数据模型进行过早的估计。在本文中，我们报告了一种新的基于自参考的分辨率估计协议，称为SRes，该协议仅需要一个重构的3D地图。SRes的核心思想是通过对地图进行分割的多个尺寸可变掩码对地图执行多尺度光谱分析（MSSA）。MSSA衍生的多尺度频谱信噪比（mSSNRs）显示，其相应的估计分辨率将显示出悬崖跳变现象，表明SSNR属性发生了重大变化。悬崖边界线上的临界点被证明是地图分辨率的正确估算者。MSSA衍生的多尺度频谱信噪比（mSSNRs）显示，其相应的估计分辨率将显示出悬崖跳变现象，表明SSNR属性发生了重大变化。悬崖边界线上的临界点被证明是地图分辨率的正确估算者。MSSA衍生的多尺度频谱信噪比（mSSNRs）显示，其相应的估计分辨率将显示出悬崖跳变现象，表明SSNR属性发生了重大变化。悬崖边界线上的临界点被证明是地图分辨率的正确估算者。

更新日期：2018-05-21

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