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Cryo-EM and Molecules: Current Progress and Perspective
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Cryo-EM and Molecules: Current Progress and Perspective

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 14915

Special Issue Editors

Prof. Dr. Weontae Lee

E-Mail Website
Guest Editor
Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
Interests: structure-function of oncogenic proteins, GPCR and proteogylycans; structural biology; protein dynamics; structure-based drug design; protein biochemistry; X-ray free electron crystallography
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Ji-Joon Song

E-Mail Website
Guest Editor
Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehakro, Daejeon 34141, Korea
Interests: chromatin biology; epigenetics; neurodegenerative disease; cryo-electron microscopy; integratgive structural approach

Special Issue Information

Dear Colleagues,

Electron microscopy (EM) is one of the oldest methods to determine protein structures and provide initial insights into the structures of large biomolecular complexes, such as ribosome and proteasome. The recent revolution of resolution in cryo-EM has tremendously enhanced our ability to examine the structures of large protein complexes in atomic details, which a was huge challenge or almost impossible using other conventional methods.

The whole structural biology community has now shifted toward using cryo-EM to determine protein structure, resulting in the number of protein structures newly deposited in PDB databases by cryo-EM exceeding that by X-ray crystallography. This is truly the era of Renaissance in structural biology, and cryo-EM will continue to play a major role in investigating the mechanism of protein complexes. Furthermore, cryo-electron tomography (Cryo-ET) combined with other optical microscopic tools has begun to emerge as an excellent or maybe the sole tool to investigate protein structures in near-atomic resolution without taking proteins out of cells.

In this Special Issue, we will highlight several important discoveries by cryo-EM and discuss future perspectives of the after-revolution era.

Prof. Dr. Weontae Lee
Prof. Dr. Ji-Joon Song
Guest Editors

Manuscript Submission Information

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Keywords

  • Structure
  • Mechanism
  • Atomic resolution
  • Electron microscopy
  • Electron tomography

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Published Papers (4 papers)

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Research

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17 pages, 33419 KiB  
Article
Sub-3 Å Cryo-EM Structures of Necrosis Virus Particles via the Use of Multipurpose TEM with Electron Counting Camera
by Chun-Hsiung Wang, Dong-Hua Chen, Shih-Hsin Huang, Yi-Min Wu, Yi-Yun Chen, Yeukuang Hwu, David Bushnell, Roger Kornberg and Wei-Hau Chang
Int. J. Mol. Sci. 2021, 22(13), 6859; https://doi.org/10.3390/ijms22136859 - 25 Jun 2021
Cited by 4 | Viewed by 4008
Abstract
During this global pandemic, cryo-EM has made a great impact on the structure determination of COVID-19 proteins. However, nearly all high-resolution results are based on data acquired on state-of-the-art microscopes where their availability is restricted to a number of centers across the globe [...] Read more.
During this global pandemic, cryo-EM has made a great impact on the structure determination of COVID-19 proteins. However, nearly all high-resolution results are based on data acquired on state-of-the-art microscopes where their availability is restricted to a number of centers across the globe with the studies on infectious viruses being further regulated or forbidden. One potential remedy is to employ multipurpose microscopes. Here, we investigated the capability of 200 kV multipurpose microscopes equipped with a direct electron camera in determining the structures of infectious particles. We used 30 nm particles of the grouper nerve necrosis virus as a test sample and obtained the cryo-EM structure with a resolution as high as ∼2.7 Å from a setting that used electron counting. For comparison, we tested a high-end cryo-EM (Talos Arctica) using a similar virus (Macrobrachium rosenbergii nodavirus) to obtain virtually the same resolution. Those results revealed that the resolution is ultimately limited by the depth of field. Our work updates the density maps of these viruses at the sub-3Å level to allow for building accurate atomic models from de novo to provide structural insights into the assembly of the capsids. Importantly, this study demonstrated that multipurpose TEMs are capable of the high-resolution cryo-EM structure determination of infectious particles and is thus germane to the research on pandemics. Full article
(This article belongs to the Special Issue Cryo-EM and Molecules: Current Progress and Perspective)
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9 pages, 2505 KiB  
Article
Structural Fluctuations of the Human Proteasome α7 Homo-Tetradecamer Double Ring Imply the Proteasomal α-Ring Assembly Mechanism
by Chihong Song, Tadashi Satoh, Taichiro Sekiguchi, Koichi Kato and Kazuyoshi Murata
Int. J. Mol. Sci. 2021, 22(9), 4519; https://doi.org/10.3390/ijms22094519 - 26 Apr 2021
Cited by 1 | Viewed by 2398
Abstract
The 20S proteasome, which is composed of layered α and β heptameric rings, is the core complex of the eukaryotic proteasome involved in proteolysis. The α7 subunit is a component of the α ring, and it self-assembles into a homo-tetradecamer consisting of two [...] Read more.
The 20S proteasome, which is composed of layered α and β heptameric rings, is the core complex of the eukaryotic proteasome involved in proteolysis. The α7 subunit is a component of the α ring, and it self-assembles into a homo-tetradecamer consisting of two layers of α7 heptameric rings. However, the structure of the α7 double ring in solution has not been fully elucidated. We applied cryo-electron microscopy to delineate the structure of the α7 double ring in solution, revealing a structure different from the previously reported crystallographic model. The D7-symmetrical double ring was stacked with a 15° clockwise twist and a separation of 3 Å between the two rings. Two more conformations, dislocated and fully open, were also identified. Our observations suggest that the α7 double-ring structure fluctuates considerably in solution, allowing for the insertion of homologous α subunits, finally converting to the hetero-heptameric α rings in the 20S proteasome. Full article
(This article belongs to the Special Issue Cryo-EM and Molecules: Current Progress and Perspective)
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Review

Jump to: Research

14 pages, 2081 KiB  
Review
Coming of Age: Cryo-Electron Tomography as a Versatile Tool to Generate High-Resolution Structures at Cellular/Biological Interfaces
by Zuoneng Wang, Qingyang Zhang and Carsten Mim
Int. J. Mol. Sci. 2021, 22(12), 6177; https://doi.org/10.3390/ijms22126177 - 8 Jun 2021
Cited by 6 | Viewed by 4087
Abstract
Over the last few years, cryo electron microscopy has become the most important method in structural biology. While 80% of deposited maps are from single particle analysis, electron tomography has grown to become the second most important method. In particular sub-tomogram averaging has [...] Read more.
Over the last few years, cryo electron microscopy has become the most important method in structural biology. While 80% of deposited maps are from single particle analysis, electron tomography has grown to become the second most important method. In particular sub-tomogram averaging has matured as a method, delivering structures between 2 and 5 Å from complexes in cells as well as in vitro complexes. While this resolution range is not standard, novel developments point toward a promising future. Here, we provide a guide for the workflow from sample to structure to gain insight into this emerging field. Full article
(This article belongs to the Special Issue Cryo-EM and Molecules: Current Progress and Perspective)
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21 pages, 2303 KiB  
Review
Recent Advances in Single-Particle Electron Microscopic Analysis of Autophagy Degradation Machinery
by Yiu Wing Sunny Cheung, Sung-Eun Nam and Calvin K. Yip
Int. J. Mol. Sci. 2020, 21(21), 8051; https://doi.org/10.3390/ijms21218051 - 28 Oct 2020
Cited by 1 | Viewed by 3298
Abstract
Macroautophagy (also known as autophagy) is a major pathway for selective degradation of misfolded/aggregated proteins and damaged organelles and non-selective degradation of cytoplasmic constituents for the generation of power during nutrient deprivation. The multi-step degradation process, from sequestering cytoplasmic cargo into the double-membrane [...] Read more.
Macroautophagy (also known as autophagy) is a major pathway for selective degradation of misfolded/aggregated proteins and damaged organelles and non-selective degradation of cytoplasmic constituents for the generation of power during nutrient deprivation. The multi-step degradation process, from sequestering cytoplasmic cargo into the double-membrane vesicle termed autophagosome to the delivery of the autophagosome to the lysosome or lytic vacuole for breakdown, is mediated by the core autophagy machinery composed of multiple Atg proteins, as well as the divergent sequence family of selective autophagy receptors. Single-particle electron microscopy (EM) is a molecular imaging approach that has become an increasingly important tool in the structural characterization of proteins and macromolecular complexes. This article summarizes the contributions single-particle EM have made in advancing our understanding of the core autophagy machinery and selective autophagy receptors. We also discuss current technical challenges and roadblocks, as well as look into the future of single-particle EM in autophagy research. Full article
(This article belongs to the Special Issue Cryo-EM and Molecules: Current Progress and Perspective)
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