Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions

被引：77
作者：
Zhu, Dongjie [1 ,2 ]
Wang, Xiangxi [1 ]
Fang, Qianglin [3 ]
Van Etten, James L. [4 ,5 ]
Rossmann, Michael G. [3 ]
Rao, Zihe [1 ,6 ,7 ]
Zhang, Xinzheng [1 ,6 ,8 ]
机构：
[1] Chinese Acad Sci, Inst Biophys, CAS Ctr Excellence Biomacromol, Natl Lab Biomacromol, Beijing 100101, Peoples R China
[2] Univ Sci & Technol China, Sch Life Sci, Hefei 230026, Anhui, Peoples R China
[3] Purdue Univ, Dept Biol Sci, 240 South Martin Jischke Dr, W Lafayette, IN 47907 USA
[4] Univ Nebraska, Dept Plant Pathol, Lincoln, NE 68583 USA
[5] Univ Nebraska, Nebraska Ctr Virol, Lincoln, NE 68583 USA
[6] Univ Chinese Acad Sci, Beijing 100049, Peoples R China
[7] Tsinghua Univ, Sch Med, Lab Struct Biol, Beijing 100084, Peoples R China
[8] Chinese Acad Sci, Inst Biophys, CAS Ctr Excellence Biomacromol, Ctr Biol Imaging, Beijing 100101, Peoples R China
来源：
NATURE COMMUNICATIONS | 2018年 / 9卷
基金：
美国国家卫生研究院; 国家重点研发计划;
关键词：
ANGSTROM RESOLUTION; ELECTRON-MICROSCOPY; CRYOELECTRON MICROSCOPY; ATOMIC-STRUCTURE; CTF CORRECTION; VIRUSES; COMPLEX; CRYOMICROSCOPY; MICROGRAPHS; IMPROVES;
D O I：
10.1038/s41467-018-04051-9
中图分类号：
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a reconstruction. Here we estimate the attainable resolution and report a "block-based" reconstruction method for extending the resolution limit. We find the Ewald sphere effect limits the resolution of large objects, especially large viruses. After processing two real datasets of large viruses, we show that our procedure can extend the resolution for both datasets and can accommodate the flexibility associated with large protein complexes.
引用
收藏
页数：7
相关论文
共 50 条
  • [31] The Ewald sphere/focus gradient does not limit the resolution of cryoEM reconstructions
    Heymann, J. Bernard
    JOURNAL OF STRUCTURAL BIOLOGY-X, 2023, 7
  • [32] Current outcomes when optimizing 'standard' sample preparation for single-particle cryo-EM
    Carragher, B.
    Cheng, Y.
    Frost, A.
    Glaeser, R. M.
    Lander, G. C.
    Nogales, E.
    Wang, H-W
    JOURNAL OF MICROSCOPY, 2019, 276 (01) : 39 - 45
  • [33] Data-driven determination of number of discrete conformations in single-particle cryo-EM
    Zhou, Ye
    Moscovich, Amit
    Bartesaghi, Alberto
    COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, 2022, 221
  • [34] New tools for automated cryo-EM single-particle analysis in RELION-4.0
    Kimanius, Dari
    Dong, Liyi
    Sharov, Grigory
    Nakane, Takanori
    Scheres, Sjors H. W.
    BIOCHEMICAL JOURNAL, 2021, 478 (24) : 4169 - 4185
  • [35] Single-particle reconstruction statistics: a diagnostic tool in solving biomolecular structures by cryo-EM
    Heymann, J. Bernard
    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2019, 75 : 33 - 44
  • [36] Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components
    Yu, Guimei
    Yan, Rui
    Zhang, Chuan
    Mao, Chengde
    Jiang, Wen
    SMALL, 2015, 11 (38) : 5157 - 5163
  • [37] Single-particle cryo-EM structure of a voltage-activated potassium channel in lipid nanodiscs
    Matthies, Doreen
    Bae, Chanhyung
    Toombes, Gilman E. S.
    Fox, Tara
    Bartesaghi, Alberto
    Subramaniam, Sriram
    Swartz, Kenton Jon
    ELIFE, 2018, 7
  • [38] Perspective: Biochemical and Physical Constraints Associated With Preparing Thin Specimens for Single-Particle Cryo-EM
    Han, Bong-Gyoon
    Armstrong, Max
    Fletcher, Daniel A.
    Glaeser, Robert M.
    FRONTIERS IN MOLECULAR BIOSCIENCES, 2022, 9
  • [39] Benchmarking cryo-EM Single Particle Analysis Workflow
    Kim, Laura Y.
    Rice, William J.
    Eng, Edward T.
    Kopylov, Mykhailo
    Cheng, Anchi
    Raczkowski, Ashleigh M.
    Jordan, Kelsey D.
    Bobe, Daija
    Potter, Clinton S.
    Carragher, Bridget
    FRONTIERS IN MOLECULAR BIOSCIENCES, 2018, 5
  • [40] Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
    Li, Xueming
    Mooney, Paul
    Zheng, Shawn
    Booth, Christopher R.
    Braunfeld, Michael B.
    Gubbens, Sander
    Agard, David A.
    Cheng, Yifan
    NATURE METHODS, 2013, 10 (06) : 584 - +
12345