Acid-Stable Capsid Structure of  <i>Helicobacter Pylori</i> Bacteriophage KHP30 by Single-Particle Cryo-Electron Microscopy

Cryo–electron microscopy, or simply cryo-EM, refers mainly to three very different yet closely related techniques: electron crystallography, single-particle cryo-EM, and electron cryotomography. In the past few years, single-particle cryo-EM in particular has triggered a revolution in structural biology and has become a newly dominant discipline. This Review examines the fascinating story of its start and evolution over the past 40-plus years, delves into how and why the recent technological advances have been so groundbreaking, and briefly considers where the technique may be headed in the future.

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In situ structure determination using single particle cryo-electron microscopy images

10.1101/2020.09.04.282509 ◽

2020 ◽

Author(s):

Jing Cheng ◽

Bufan Li ◽

Long Si ◽

Xinzheng Zhang

Keyword(s):

Electron Microscopy ◽

Structure Determination ◽

Single Particle ◽

Structure Refinement ◽

Target Function ◽

Target Protein ◽

Particle Analysis ◽

Cryo Electron Microscopy ◽

Tilt Series

AbstractCryo-electron microscopy (cryo-EM) tomography is a powerful tool for in situ structure determination. However, this method requires the acquisition of tilt series, and its time consuming throughput of acquiring tilt series severely slows determination of in situ structures. By treating the electron densities of non-target protein as non-Gaussian distributed noise, we developed a new target function that greatly improves the efficiency of the recognition of the target protein in a single cryo-EM image without acquiring tilt series. Moreover, we developed a sorting function that effectively eliminates the false positive detection, which not only improves the resolution during the subsequent structure refinement procedure but also allows using homolog proteins as models to recognize the target protein. Together, we developed an in situ single particle analysis (isSPA) method. Our isSPA method was successfully applied to solve structures of glycoproteins on the surface of a non-icosahedral virus and Rubisco inside the carboxysome. The cryo-EM data from both samples were collected within 24 hours, thus allowing fast and simple structural determination in situ.

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Recent Developments of Single Particle Analysis with Cryo-electron Microscopy

Nihon Kessho Gakkaishi ◽

10.5940/jcrsj.60.230 ◽

2018 ◽

Vol 60 (5-6) ◽

pp. 230-232

Author(s):

Takanori NAKANE

Keyword(s):

Electron Microscopy ◽

Single Particle ◽

Particle Analysis ◽

Single Particle Analysis ◽

Cryo Electron Microscopy ◽

Recent Developments

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A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy

Nature Communications ◽

10.1038/s41467-017-00718-x ◽

2017 ◽

Vol 8 (1) ◽

Cited By ~ 27

Author(s):

Linda E. Franken ◽

Gert T. Oostergetel ◽

Tjaard Pijning ◽

Pranav Puri ◽

Valentina Arkhipova ◽

...

Keyword(s):

Electron Microscopy ◽

Single Particle ◽

General Mechanism ◽

Cryo Electron Microscopy

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Using Molecular Dynamics Simulations to Compare the Stability of Lysenin Structures Obtained through X-ray Crystallography and Single-Particle Cryo-Electron Microscopy

Biophysical Journal ◽

10.1016/j.bpj.2017.11.1883 ◽

2018 ◽

Vol 114 (3) ◽

pp. 337a

Author(s):

Vivek Govind Kumar

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Single Particle ◽

X Ray ◽

X Ray Crystallography ◽

Cryo Electron Microscopy ◽

The Stability ◽

Dynamics Simulations

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How Good Can Single-Particle Cryo-EM Become? What Remains Before It Approaches Its Physical Limits?

Annual Review of Biophysics ◽

10.1146/annurev-biophys-070317-032828 ◽

2019 ◽

Vol 48 (1) ◽

pp. 45-61 ◽

Cited By ~ 26

Author(s):

Robert M. Glaeser

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

Single Particle ◽

Energy Use ◽

Optimal Choice ◽

Structural Basis ◽

Detective Quantum Efficiency ◽

Quantum Metrology ◽

Cryo Electron Microscopy ◽

Induced Motion

Impressive though the achievements of single-particle cryo–electron microscopy are today, a substantial gap still remains between what is currently accomplished and what is theoretically possible. As is reviewed here, twofold or more improvements are possible as regards ( a) the detective quantum efficiency of cameras at high resolution, ( b) converting phase modulations to intensity modulations in the image, and ( c) recovering the full amount of high-resolution signal in the presence of beam-induced motion of the specimen. In addition, potential for improvement is reviewed for other topics such as optimal choice of electron energy, use of aberration correctors, and quantum metrology. With the help of such improvements, it does not seem to be too much to imagine that determining the structural basis for every aspect of catalytic control, signaling, and regulation, in any type of cell of interest, could easily be accelerated fivefold or more.

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