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Journal articles on the topic 'Cryo-EM structure'

Author: Grafiati

Published: 7 June 2025

Last updated: 17 July 2025

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1

Rohou, Alexis. "Improving cryo-EM structure validation." Nature Methods 18, no. 2 (2021): 130–31. http://dx.doi.org/10.1038/s41592-021-01062-1.

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2

Powell, Samantha, and James Evans. "Cryo-EM Protein Structure Without Purification." Structural Dynamics 12, no. 2_Supplement (2025): A151. https://doi.org/10.1063/4.0000460.

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Determining protein structures can be a laborious and time-consuming process. Despite recent advances in single particle cryo- electron microscopy (cryo-EM) which have reduced the timeline for structure determination, one of the largest remaining bottlenecks is sample preparation. Traditionally, most single particle cryo-EM workflows rely on obtaining a highly homogenous and pure sample to yield a high-resolution protein structure, but protein expression and purification can be time-consuming and often challenging steps. To combat this, other groups have developed affinity grids using a variet

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Kimanius, Dari, Gustav Zickert, Takanori Nakane, et al. "Exploiting prior knowledge about biological macromolecules in cryo-EM structure determination." IUCrJ 8, no. 1 (2021): 60–75. http://dx.doi.org/10.1107/s2052252520014384.

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Three-dimensional reconstruction of the electron-scattering potential of biological macromolecules from electron cryo-microscopy (cryo-EM) projection images is an ill-posed problem. The most popular cryo-EM software solutions to date rely on a regularization approach that is based on the prior assumption that the scattering potential varies smoothly over three-dimensional space. Although this approach has been hugely successful in recent years, the amount of prior knowledge that it exploits compares unfavorably with the knowledge about biological structures that has been accumulated over decad

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García-Nafría, Javier, and Christopher G. Tate. "Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development." Annual Review of Pharmacology and Toxicology 60, no. 1 (2020): 51–71. http://dx.doi.org/10.1146/annurev-pharmtox-010919-023545.

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Electron cryo-microscopy (cryo-EM) has revolutionized structure determination of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallography. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein–coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiolog

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Zeng, Lingxiao, Wei Ding, and Quan Hao. "Using cryo-electron microscopy maps for X-ray structure determination of homologues." Acta Crystallographica Section D Structural Biology 76, no. 1 (2020): 63–72. http://dx.doi.org/10.1107/s2059798319015924.

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The combination of cryo-electron microscopy (cryo-EM) and X-ray crystallography reflects an important trend in structural biology. In a previously published study, a hybrid method for the determination of X-ray structures using initial phases provided by the corresponding parts of cryo-EM maps was presented. However, if the target structure of X-ray crystallography is not identical but homologous to the corresponding molecular model of the cryo-EM map, then the decrease in the accuracy of the starting phases makes the whole process more difficult. Here, a modified hybrid method is presented to

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Stewart, P. L., and G. R. Nemerow. "Combining structures from cryo-EM and x-ray crystallography." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 44–45. http://dx.doi.org/10.1017/s0424820100136593.

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Cryo-electron microscopy (cryo-EM) combined with three-dimensional image reconstruction techniques has produced structures of large macromolecular assemblies. Interpretation of low resolution (25-35 A) cryo-EM density can be greatly enhanced by mapping in crystallographic structures of component molecules. Difference imaging between the cryo-EM structure of the human adenovirus particle and a capsid calculated from the crystal structure of the major structural protein, hexon, revealed numerous minor structural components in the viral capsid. In addition, the atomic binding sites of the minor p

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Punjani, Ali. "Real-time cryo-EM structure determination." Microscopy and Microanalysis 27, S1 (2021): 1156–57. http://dx.doi.org/10.1017/s1431927621004360.

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8

Dai, Muzhi, Zhuoer Dong, Weining Fu, Kui Xu, and Qiangfeng Cliff Zhang. "CryoDomain: Sequence-free Protein Domain Identification from Low-resolution Cryo-EM Density Maps." Proceedings of the AAAI Conference on Artificial Intelligence 39, no. 1 (2025): 119–27. https://doi.org/10.1609/aaai.v39i1.31987.

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Cryo-electron microscopy (cryo-EM) has revolutionized the field of structural biology, determining structures of large protein machines and sharpening the understanding of fundamental biological processes. Despite cryo-EM’s unique capacity to discover novel proteins from unpurified samples and reveal the intricate structures of protein complexes within native cellular environments, the advancement of protein identification methods for cryo-EM lags behind. Without prior knowledge, such as sequence, protein identification from low-resolution density maps remains challenging. Here we introduce Cr

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Henderson, Richard, and Samar Hasnain. "`Cryo-EM': electron cryomicroscopy, cryo electron microscopy or something else?" IUCrJ 10, no. 5 (2023): 519–20. http://dx.doi.org/10.1107/s2052252523006759.

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Structural biology continues to benefit from an expanding toolkit, which is helping to gain unprecedented insight into the assembly and organization of multi-protein machineries, enzyme mechanisms and ligand/inhibitor binding. During the last ten years, cryoEM has become widely available and has provided a major boost to structure determination of membrane proteins and large multi-protein complexes. Many of the structures have now been made available at resolutions around 2 Å, where fundamental questions regarding enzyme mechanisms can be addressed. Over the years, the abbreviation cryoEM has

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10

Zeng, Lingxiao, Wei Ding, and Quan Hao. "Using cryo-electron microscopy maps for X-ray structure determination." IUCrJ 5, no. 4 (2018): 382–89. http://dx.doi.org/10.1107/s2052252518005857.

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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 pha

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Stojković, Vanja, Alexander G. Myasnikov, Iris D. Young, Adam Frost, James S. Fraser, and Danica Galonić Fujimori. "Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit." Nucleic Acids Research 48, no. 5 (2020): 2723–32. http://dx.doi.org/10.1093/nar/gkaa037.

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Abstract Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides’ positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cry

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Boland, Andreas, Leifu Chang, and David Barford. "The potential of cryo-electron microscopy for structure-based drug design." Essays in Biochemistry 61, no. 5 (2017): 543–60. http://dx.doi.org/10.1042/ebc20170032.

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Structure-based drug design plays a central role in therapeutic development. Until recently, protein crystallography and NMR have dominated experimental approaches to obtain structural information of biological molecules. However, in recent years rapid technical developments in single particle cryo-electron microscopy (cryo-EM) have enabled the determination to near-atomic resolution of macromolecules ranging from large multi-subunit molecular machines to proteins as small as 64 kDa. These advances have revolutionized structural biology by hugely expanding both the range of macromolecules whos

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García-Nafría, Javier, and Christopher G. Tate. "Structure determination of GPCRs: cryo-EM compared with X-ray crystallography." Biochemical Society Transactions 49, no. 5 (2021): 2345–55. http://dx.doi.org/10.1042/bst20210431.

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G protein-coupled receptors (GPCRs) are the largest single family of cell surface receptors encoded by the human genome and they play pivotal roles in co-ordinating cellular systems throughout the human body, making them ideal drug targets. Structural biology has played a key role in defining how receptors are activated and signal through G proteins and β-arrestins. The application of structure-based drug design (SBDD) is now yielding novel compounds targeting GPCRs. There is thus significant interest from both academia and the pharmaceutical industry in the structural biology of GPCRs as curr

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Behkamal, Bahareh, Mahmoud Naghibzadeh, Mohammad Reza Saberi, Zeinab Amiri Tehranizadeh, Andrea Pagnani, and Kamal Al Nasr. "Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps." Biomolecules 11, no. 12 (2021): 1773. http://dx.doi.org/10.3390/biom11121773.

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Cryo-electron microscopy (cryo-EM) is a structural technique that has played a significant role in protein structure determination in recent years. Compared to the traditional methods of X-ray crystallography and NMR spectroscopy, cryo-EM is capable of producing images of much larger protein complexes. However, cryo-EM reconstructions are limited to medium-resolution (~4–10 Å) for some cases. At this resolution range, a cryo-EM density map can hardly be used to directly determine the structure of proteins at atomic level resolutions, or even at their amino acid residue backbones. At such a res

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Fàbrega-Ferrer, Montserrat, Ana Cuervo, Francisco J. Fernández, et al. "Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure." Acta Crystallographica Section D Structural Biology 77, no. 1 (2021): 11–18. http://dx.doi.org/10.1107/s2059798320015156.

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Medium-resolution cryo-electron microscopy maps, in particular when they include a significant number of α-helices, may allow the building of partial models that are useful for molecular-replacement searches in large crystallographic structures when the structures of homologs are not available and experimental phasing has failed. Here, as an example, the solution of the structure of a bacteriophage portal using a partial 30% model built into a 7.8 Å resolution cryo-EM map is shown. Inspection of the self-rotation function allowed the correct oligomerization state to be determined, and density-

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Chandra, Mintu, Amy K. Kendall, and Lauren P. Jackson. "Unveiling the cryo-EM structure of retromer." Biochemical Society Transactions 48, no. 5 (2020): 2261–72. http://dx.doi.org/10.1042/bst20200552.

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Retromer (VPS26/VPS35/VPS29) is a highly conserved eukaryotic protein complex that localizes to endosomes to sort transmembrane protein cargoes into vesicles and elongated tubules. Retromer mediates retrieval pathways from endosomes to the trans-Golgi network in all eukaryotes and further facilitates recycling pathways to the plasma membrane in metazoans. In cells, retromer engages multiple partners to orchestrate the formation of tubulovesicular structures, including sorting nexin (SNX) proteins, cargo adaptors, GTPases, regulators, and actin remodeling proteins. Retromer-mediated pathways ar

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Chari, Ashwin, and Holger Stark. "Prospects and Limitations of High-Resolution Single-Particle Cryo-Electron Microscopy." Annual Review of Biophysics 52, no. 1 (2023): 391–411. http://dx.doi.org/10.1146/annurev-biophys-111622-091300.

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Single particle cryo-electron microscopy (cryo-EM) has matured into a robust method for the determination of biological macromolecule structures in the past decade, complementing X-ray crystallography and nuclear magnetic resonance. Constant methodological improvements in both cryo-EM hardware and image processing software continue to contribute to an exponential growth in the number of structures solved annually. In this review, we provide a historical view of the many steps that were required to make cryo-EM a successful method for the determination of high-resolution protein complex structu

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18

Chirigati, Fernando. "Predicting protein structure from cryo-EM data." Nature Computational Science 1, no. 2 (2021): 96. http://dx.doi.org/10.1038/s43588-021-00035-w.

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19

Wang, Ivy, Sandeep K. Gupta, Guillaume Ems, Nadishka Jayawardena, Mike Strauss, and Mihnea Bostina. "Cryo-EM Structure of a Possum Enterovirus." Viruses 14, no. 2 (2022): 318. http://dx.doi.org/10.3390/v14020318.

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Enteroviruses (EVs) represent a substantial concern to global health. Here, we present the cryo-EM structure of a non-human enterovirus, EV-F4, isolated from the Australian brushtail possum to assess the structural diversity of these picornaviruses. The capsid structure, determined to ~3 Å resolution by single particle analysis, exhibits a largely smooth surface, similar to EV-F3 (formerly BEV-2). Although the cellular receptor is not known, the absence of charged residues on the outer surface of the canyon suggest a different receptor type than for EV-F3. Density for the pocket factor is clea

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20

MATSUNAMI, Hideyuki. "Cryo-EM Structure of Campylobacter Flagellar Hook." Seibutsu Butsuri 57, no. 5 (2017): 265–67. http://dx.doi.org/10.2142/biophys.57.265.

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21

Feng, Yangyang, Yuan Tian, Zihan Wu, and Yanhui Xu. "Cryo-EM structure of human SRCAP complex." Cell Research 28, no. 11 (2018): 1121–23. http://dx.doi.org/10.1038/s41422-018-0102-y.

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22

Mei, Kunrong, Yan Li, Shaoxiao Wang, et al. "Cryo-EM structure of the exocyst complex." Nature Structural & Molecular Biology 25, no. 2 (2018): 139–46. http://dx.doi.org/10.1038/s41594-017-0016-2.

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23

Di Cera, Enrico. "Another cryo-EM success: structure of FXIII." Blood 145, no. 4 (2025): 356–57. https://doi.org/10.1182/blood.2024027405.

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24

Yang, C., G. Ji, H. Liu, et al. "Cryo-EM structure of a transcribing cypovirus." Proceedings of the National Academy of Sciences 109, no. 16 (2012): 6118–23. http://dx.doi.org/10.1073/pnas.1200206109.

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Zheng, Weili, Caitlin N. Spaulding, Henry L. Schreiber, et al. "Cryo-Em Structure of Type 1 Pilus." Biophysical Journal 114, no. 3 (2018): 370a. http://dx.doi.org/10.1016/j.bpj.2017.11.2052.

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26

Poweleit, Nicole, Claudio Catalano, Kyle Lucier, et al. "Leveraging Advances in Cryo Electron Microscopy to Facilitate Drug Discovery." Structural Dynamics 12, no. 2_Supplement (2025): A361. https://doi.org/10.1063/4.0000667.

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Getting a new therapeutic to market can take years and millions of dollars in funding for research and development, clinical trials, and drug production. Structure based drug design is a helpful tool in the pre-clinical research and development process to improve drug candidates. Cryo-EM is increasingly utilized among a suite of structural biology techniques to elucidate structures of target proteins in complex with therapeutic drugs and antibodies. However, challenges to determining cryo-EM structures of therapeutic targets remain including sample size limitations and preferred orientation. H

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Sharif, Humayun, Yang Li, Yuanchen Dong, et al. "Cryo-EM structure of the DNA-PK holoenzyme." Proceedings of the National Academy of Sciences 114, no. 28 (2017): 7367–72. http://dx.doi.org/10.1073/pnas.1707386114.

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DNA-dependent protein kinase (DNA-PK) is a large protein complex central to the nonhomologous end joining (NHEJ) DNA-repair pathway. It comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer of DNA-binding proteins Ku70 and Ku80. Here, we report the cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs at 4.4-Å resolution and the DNA-PK holoenzyme at 5.8-Å resolution. The DNA-PKcs structure contains three distinct segments: the N-terminal region with an arm and a bridge, the circular cradle, and the head that includes the kinase domain. Two perpendicular apertures exis

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Mazhab-Jafari, Mohammad T., and John L. Rubinstein. "Cryo-EM studies of the structure and dynamics of vacuolar-type ATPases." Science Advances 2, no. 7 (2016): e1600725. http://dx.doi.org/10.1126/sciadv.1600725.

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Electron cryomicroscopy (cryo-EM) has significantly advanced our understanding of molecular structure in biology. Recent innovations in both hardware and software have made cryo-EM a viable alternative for targets that are not amenable to x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Cryo-EM has even become the method of choice in some situations where x-ray crystallography and NMR spectroscopy are possible but where cryo-EM can determine structures at higher resolution or with less time or effort. Rotary adenosine triphosphatases (ATPases) are crucial to the maintena

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Samygina, Valeria, Eugene Pichkur, Peter Cherepanov, Alexey Egorov, Aydar Ishmukhametov, and Michail Vorovich. "Abstract OR-8: Cryo-EM Structure of Mature Yellow Fever Virus." International Journal of Biomedicine 11, Suppl_1 (2021): S10. http://dx.doi.org/10.21103/ijbm.11.suppl_1.or8.

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Background: Yellow fever virus (YFV) is the prototype virus of the genus Flavivirus. It is endemic to sub-Saharan Africa and tropical South America. YF disease ranges from asymptomatic to severe jaundice and hemorrhagic fever. The flavivirus virion core is enveloped by a lipid membrane with integrated membrane (M) proteins and envelope (E) proteins that form the outer surface of the virion. The Е protein provides stability to the viral particle and is responsible for early infection stages. Flaviviruses are heterogeneous in nature, which is related to their maturation process. Samples always c

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Wendler, Petra, and Helen R. Saibil. "Cryo electron microscopy structures of Hsp100 proteins: crowbars in or out?This paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process." Biochemistry and Cell Biology 88, no. 1 (2010): 89–96. http://dx.doi.org/10.1139/o09-164.

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Independent cryo electron microscopy (cryo-EM) studies of the closely related protein disaggregases ClpB and Hsp104 have resulted in two different models of subunit arrangement in the active hexamer. We compare the EM maps and resulting atomic structure fits, discuss their differences, and relate them to published experimental information in an attempt to discriminate between models. In addition, we present some general assessment criteria for low-resolution cryo-EM maps to offer non-structural biologists tools to evaluate these structures.

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Chen, Lin, Brandon Baker, Eduardo Santos, Michell Sheep, and Darius Daftarian. "A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform." Medicines 6, no. 3 (2019): 86. http://dx.doi.org/10.3390/medicines6030086.

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Background: Cryo-electron microscopy (cryo-EM) has become a major technique for protein structure determination. However, due to the low quality of cryo-EM density maps, many protein structures derived from cryo-EM contain outliers introduced during the modeling process. The current protein model validation system lacks identification features for cryo-EM proteins making it not enough to identify outliers in cryo-EM proteins. Methods: This study introduces an efficient unsupervised outlier detection model for validating protein models built from cryo-EM technique. The current model uses a high

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Manka, Szymon W., and Carolyn A. Moores. "Microtubule structure by cryo-EM: snapshots of dynamic instability." Essays in Biochemistry 62, no. 6 (2018): 737–51. http://dx.doi.org/10.1042/ebc20180031.

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The development of cryo-electron microscopy (cryo-EM) allowed microtubules to be captured in their solution-like state, enabling decades of insight into their dynamic mechanisms and interactions with binding partners. Cryo-EM micrographs provide 2D visualization of microtubules, and these 2D images can also be used to reconstruct the 3D structure of the polymer and any associated binding partners. In this way, the binding sites for numerous components of the microtubule cytoskeleton—including motor domains from many kinesin motors, and the microtubule-binding domains of dynein motors and an ex

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Kochovski, Zdravko, Guosong Chen, Jiayin Yuan, and Yan Lu. "Cryo-Electron microscopy for the study of self-assembled poly(ionic liquid) nanoparticles and protein supramolecular structures." Colloid and Polymer Science 298, no. 7 (2020): 707–17. http://dx.doi.org/10.1007/s00396-020-04657-w.

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Abstract Cryo-electron microscopy (cryo-EM) is a powerful structure determination technique that is well-suited to the study of protein and polymer self-assembly in solution. In contrast to conventional transmission electron microscopy (TEM) sample preparation, which often times involves drying and staining, the frozen-hydrated sample preparation allows the specimens to be kept and imaged in a state closest to their native one. Here, we give a short overview of the basic principles of Cryo-EM and review our results on applying it to the study of different protein and polymer self-assembled nan

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Roh, Soung-Hun, Corey F. Hryc, Hyun-Hwan Jeong, et al. "Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM." Proceedings of the National Academy of Sciences 114, no. 31 (2017): 8259–64. http://dx.doi.org/10.1073/pnas.1704725114.

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Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many particles with presumed identical conformations. We used a 3.5-Å cryo-EM reconstruction with imposed D7 symmetry to further analyze structural heterogeneity among chemically identical subunits in each GroEL oligomer. Focused classification of the 14 subunits in each oligomer revealed three dominant classes of subunit conformations. Each class resembled a distinct GroEL crystal structure in the Pro

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Baker, Mariah R., Guizhen Fan, and Irina I. Serysheva. "Single-particle cryo-EM of the ryanodine receptor channel." European Journal of Translational Myology 25, no. 1 (2015): 35. http://dx.doi.org/10.4081/ejtm.2015.4803.

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Ryanodine receptors (RyRs) are tetrameric ligand-gated Ca2+ release channels that are responsible for the increase of cytosolic Ca2+ concentration leading to muscle contraction. Our current understanding of RyR channel gating and regulation is greatly limited due to the lack of a high-resolution structure of the channel protein. The enormous size and unwieldy shape of Ca2+ release channels make X-ray or NMR methods difficult to apply for high-resolution structural analysis of the full-length functional channel. Single-particle electron cryo-microscopy (cryo-EM) is one of the only effective tec

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Martin, Thomas G., Tanmay A. M. Bharat, Andreas C. Joerger, et al. "Design of a molecular support for cryo-EM structure determination." Proceedings of the National Academy of Sciences 113, no. 47 (2016): E7456—E7463. http://dx.doi.org/10.1073/pnas.1612720113.

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Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there still exist ample opportunities for improvement in sample preparation. Macromolecular complexes may disassociate or adopt nonrandom orientations against the extended air–water interface that exists for a short time before the sample is frozen. We designed a hollow support structure using 3D DNA origami to protect complexes from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle, we concentrated on the transcription factor p53, which binds to specific DNA sequences on double-strande

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Jiang, Qiu-Xing, Ceng Gao, Gaya P. Yadav, Zhuoya Wang, and Shuai Yang. "Computational analysis of ligands enables near-atomic cryo-EM structure-based drug design (cryo-EM SBDD)." Biophysical Journal 123, no. 3 (2024): 184a. http://dx.doi.org/10.1016/j.bpj.2023.11.1196.

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Parvate, Amar, Evan P. Williams, Mariah K. Taylor, et al. "Diverse Morphology and Structural Features of Old and New World Hantaviruses." Viruses 11, no. 9 (2019): 862. http://dx.doi.org/10.3390/v11090862.

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To further understanding of the structure and morphology of the Orthohantavirus, family Hantaviridae, we have employed cryo-electron microscopy (cryo-EM) for three New World hantaviruses: Andes (ANDV), Sin Nombre (SNV), and Black Creek Canal (BCCV). Building upon our prior cryo-EM and cryo-tomography study of the Old World hantavirus, Hantaan virus (HTNV), we have expanded our studies to examine the entire virion population present in cell culture supernatant. Hence, in contrast to the prior cryo-EM/ET studies in which we used a polyethylene precipitation, a sucrose gradient, and a sucrose cus

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Creekmore, Benjamin C., Yi-Wei Chang, and Edward B. Lee. "The Cryo-EM Effect: Structural Biology of Neurodegenerative Disease Aggregates." Journal of Neuropathology & Experimental Neurology 80, no. 6 (2021): 514–29. http://dx.doi.org/10.1093/jnen/nlab039.

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Abstract Neurogenerative diseases are characterized by diverse protein aggregates with a variety of microscopic morphologic features. Although ultrastructural studies of human neurodegenerative disease tissues have been conducted since the 1960s, only recently have near-atomic resolution structures of neurodegenerative disease aggregates been described. Solid-state nuclear magnetic resonance spectroscopy and X-ray crystallography have provided near-atomic resolution information about in vitro aggregates but pose logistical challenges to resolving the structure of aggregates derived from human

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Baymukhametov, T. N., Yu M. Chesnokov, E. B. Pichkur, et al. "Three-Dimensional Structure of Cytochrome c Nitrite Reductase As Determined by Cryo-Electron Microscopy." Acta Naturae 10, no. 3 (2018): 48–56. http://dx.doi.org/10.32607/20758251-2018-10-3-48-56.

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The structure of cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens was determined by cryo-electron microscopy (cryo-EM) at a 2.56 resolution. Possible structural heterogeneity of the enzyme was assessed. The backbone and side-chain orientations in the cryo-EM-based model are, in general, similar to those in the high-resolution X-ray diffraction structure of this enzyme.

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Liebschner, Dorothee, Pavel V. Afonine, Nigel W. Moriarty, Billy K. Poon, Vincent B. Chen, and Paul D. Adams. "CERES: a cryo-EM re-refinement system for continuous improvement of deposited models." Acta Crystallographica Section D Structural Biology 77, no. 1 (2021): 48–61. http://dx.doi.org/10.1107/s2059798320015879.

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The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM s

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He, Jiahua, and Sheng-You Huang. "EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps." Briefings in Bioinformatics, May 5, 2021. http://dx.doi.org/10.1093/bib/bbab156.

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Abstract Cryo-electron microscopy (cryo-EM) has become one of important experimental methods in structure determination. However, despite the rapid growth in the number of deposited cryo-EM maps motivated by advances in microscopy instruments and image processing algorithms, building accurate structure models for cryo-EM maps remains a challenge. Protein secondary structure information, which can be extracted from EM maps, is beneficial for cryo-EM structure modeling. Here, we present a novel secondary structure annotation framework for cryo-EM maps at both intermediate and high resolutions, n

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Li, Shu, Genki Terashi, Zicong Zhang, and Daisuke Kihara. "Advancing structure modeling from cryo-EM maps with deep learning." Biochemical Society Transactions 53, no. 01 (2025). https://doi.org/10.1042/bst20240784.

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Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling the determination of biomolecular structures that are challenging to resolve using conventional methods. Interpreting a cryo-EM map requires accurate modeling of the structures of underlying biomolecules. Here, we concisely discuss the evolution and current state of automatic structure modeling from cryo-EM density maps. We classify modeling methods into two categories: de novo modeling methods from high-resolution maps (better than 5 Å) and methods that model by fitting individual structures of component prot

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Alnabati, Eman, Juan Esquivel-Rodriguez, Genki Terashi, and Daisuke Kihara. "MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field." Frontiers in Molecular Biosciences 9 (July 25, 2022). http://dx.doi.org/10.3389/fmolb.2022.935411.

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An increasing number of protein complex structures are determined by cryo-electron microscopy (cryo-EM). When individual protein structures have been determined and are available, an important task in structure modeling is to fit the individual structures into the density map. Here, we designed a method that fits the atomic structures of proteins in cryo-EM maps of medium to low resolutions using Markov random fields, which allows probabilistic evaluation of fitted models. The accuracy of our method, MarkovFit, performed better than existing methods on datasets of 31 simulated cryo-EM maps of

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Giri, Nabin, and Jianlin Cheng. "De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM." Nature Communications 15, no. 1 (2024). http://dx.doi.org/10.1038/s41467-024-49647-6.

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AbstractAccurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated de novo cryo-EM structure modeling method. Cryo2Struct utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps, followed by an innovative Hidden Markov Model (HMM) to connect predicted atoms and build protein back

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Kato, Koji, Naoyuki Miyazaki, Tasuku Hamaguchi, et al. "High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams." Communications Biology 4, no. 1 (2021). http://dx.doi.org/10.1038/s42003-021-01919-3.

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AbstractPhotosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Elec

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Ma, Haiyun, Xinyu Jia, Kaiming Zhang, and Zhaoming Su. "Cryo-EM advances in RNA structure determination." Signal Transduction and Targeted Therapy 7, no. 1 (2022). http://dx.doi.org/10.1038/s41392-022-00916-0.

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AbstractCryo-electron microscopy (cryo-EM) has emerged as an unprecedented tool to resolve protein structures at atomic resolution. Structural insights of biological samples not accessible by conventional X-ray crystallography and NMR can be explored with cryo-EM because measurements are carried out under near-native crystal-free conditions, and large protein complexes with conformational and compositional heterogeneity are readily resolved. RNA has remained underexplored in cryo-EM, despite its essential role in various biological processes. This review highlights current challenges and recen

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Fukuda, Yoshiyuki, Kevin Stepleton, and Takayuki Kato. "Progress in special resolution of structural analysis by cryo-EM." Microscopy, October 21, 2022. http://dx.doi.org/10.1093/jmicro/dfac053.

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Abstract Since the Human Genome Project, drug discovery via structure-based drug design and development has significantly accelerated. Therefore, generating high-resolution structural information from biological macromolecules and macromolecular complexes such as proteins and nucleic acids is paramount in structural biology, medicine, and the pharmaceutical industry. Recently, Electron cryomicroscopy (cryo-EM) has undergone a technological revolution and attracted much attention in the structure-based drug discovery pipeline. This recognition is primarily due to its ability to analyze and reco

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Cianfrocco, Michael A., and Andres E. Leschziner. "Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud." eLife 4 (May 8, 2015). http://dx.doi.org/10.7554/elife.06664.

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The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle

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Jakobi, Arjen J., Matthias Wilmanns, and Carsten Sachse. "Model-based local density sharpening of cryo-EM maps." eLife 6 (October 23, 2017). http://dx.doi.org/10.7554/elife.27131.

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Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate

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