Using cryo-electron microscopy maps for X-ray structure determination

IUCrJ

Ding, W.¹  Zeng, L.² 

[1]Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China

[2]School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong

关键词: FSEARCH;    IPCAS;    ITERATIVE PHASING;    CRYO-EM;    MODEL BUILDING;    STRUCTURE DETERMINATION;    CRYO-ELECTRON MICROSCOPY;    X-RAY CRYSTALLOGRAPHY;    PHASE PROBLEM;   

DOI  :  10.1107/S2052252518005857

学科分类：数学（综合）

来源: International Union of Crystallography

【 摘 要 】

X-ray crystallography and cryo-electron microscopy (cryo-EM) are complementary techniques for structure determination. Crystallography usually reveals more detailed information, while cryo-EM is an extremely useful technique for studying large-sized macromolecules. As the gap between the resolution of crystallography and cryo-EM data narrows, the cryo-EM map of a macromolecule could serve as an initial model to solve the phase problem of crystal diffraction for high-resolution structure determination. FSEARCH is a procedure to utilize the low-resolution molecular shape for crystallographic phasing. The IPCAS (Iterative Protein Crystal structure Automatic Solution) pipeline is an automatic direct-methods-aided dual-space iterative phasing and model-building procedure. When only an electron-density map is available as the starting point, IPCAS is capable of generating a completed model from the phases of the input map automatically, without the requirement of an initial model. In this study, a hybrid method integrating X-ray crystallography with cryo-EM to help with structure determination is presented. With a cryo-EM map as the starting point, the workflow of the method involves three steps. (1) Cryo-EM map replacement: FSEARCH is utilized to find the correct translation and orientation of the cryo-EM map in the crystallographic unit cell and generates the initial low-resolution map. (2) Phase extension: the phases calculated from the correctly placed cryo-EM map are extended to high-resolution X-ray data by non-crystallographic symmetry averaging with phenix.resolve. (3) Model building: IPCAS is used to generate an initial model using the phase-extended map and perform model completion by iteration. Four cases (the lowest cryo-EM map resolution being 6.9 Å) have been tested for the general applicability of the hybrid method, and almost complete models have been generated for all test cases with reasonable Rwork/Rfree. The hybrid method therefore provides an automated tool for X-ray structure determination using a cryo-EM map as the starting point.

【 授权许可】

CC BY