Life Science Electron Microscopy Resource Library

Introduction to cryo-EM

No matter what your stage of research, you can find resources and learning materials you need to overcome obstacles and advance your research with electron microscopy.

Cryo-EM research case studies

Understanding the complexity of cancer with cryo-EM

Untangling neurodegeneration with cryo-EM

Structural virology with cryo-EM

Case studies in integrative structural biology

Cryo-EM trends in drug discovery

Integrative structural biology: high precision 3D analysis from structure to function

Novel insights using single particle cryo-electron microscopy

Revolutionizing our understanding of cell biology with cryo-electron tomography

Cryo-EM select publications

Fighting SARS-CoV-2 with structural biology methods

 

In this comment, the authors discuss how advances in the field of structural biology, particularly in single particle cryo-EM and cryo-ET, allow scientists to obtain high-resolution structural information critical for the development of vaccines and therapeutics against emerging pathogens.

 

Zhang, J., Chen, B. Fighting SARS-CoV-2 with structural biology methods. Nat Methods 19, 381–383 (2022). https://doi.org/10.1038/s41592-022-01448-9

Cryo-EM studies of membrane proteins at 200 kV

 

In this review, the researchers highlight how 200 kV cryo-TEMs are achieving sub-3 Å resolution structures of membrane proteins and list a number of potential target structures for structure-based drug discovery efforts.

 

Thangaratnarajah C, Rheinberger J & Paulino C. Cryo-EM studies of membrane proteins at 200 keV. Current Opinion in Structural Biology 76: 102440 (2022). https://doi.org/10.1016/j.sbi.2022.102440

Cryo-EM in molecular and cellular biology

 

This review summarizes the current state of methods and results achievable by cryo-electron microscopy (cryo-EM).

 

Saibil HR (2022) Cryo-EM in molecular and cellular biology. Molecular Cell 82 : 274–284 https://doi.org/10.1016/j.molcel.2021.12.016

Cryo-EM methods

Cryo-electron tomography remote data collection and sub-tomogram averaging

 

This article provides a detailed written and video walk-through of data collection using Tomography 5 and subsequent structure determination using emClarity as it is routinely employed at eBIC (Diamond Lightsource)

 

AU Sheng Y, AU Morris K, AU Radecke J & AU Zhang P. Cryo-electron Tomography Remote Data Collection and Subtomogram Averaging. JoVE : e63923 (2022). https://doi.org/10.3791/63923

Direct cell extraction of membrane proteins for structure-function analysis

The authors describe a novel method to use cryo-EM for structure-function analyses of membrane proteins extracted directly from cells and incorporated into Salipro lipid nanoparticles.

 

Drulyte I, Gutgsell AR, Lloris-Garcerá P, Liss M, Geschwindner S, Radjainia M, Frauenfeld J & Löving R (2022) Direct Cell Extraction of Membrane Proteins for Structure-Function Analysis. bioRxiv (2022). https://doi.org/10.1101/2022.07.05.498330

MicroED structure of a protoglobin reactive carbene intermediate

 

Using the recent technological advances in MicroED, Danelius et al. determined the first structures of Aeropyrum pernix protoglobin (ApePgb) using an AlphaFold2 model for phasing.

 

Danelius E, Porter NJ, Unge J, Arnold FH & Gonen T. MicroED structure of a protoglobin reactive carbene intermediate. bioRxiv (2022) https://doi.org/10.1101/2022.10.18.512604

Cryo-plasma FIB-SEM volume imaging of biological specimens

The authors describe the use of a cryo-plasma-FIB to produce three dimensional volumes in bacteria, human cells and tissue while retaining the ability to subsequently perform targeted in-situ structural biology using cryo-electron tomography.

 

Dumoux M, Glen T, Ho EML, Perdigão LMA, Klumpe S, Yee NB -y., Farmer D, Smith JLR, Lai PYA, Bowles W, Kelley R, Plitzko JM, Wu L, Basham M, Clare DK, Siebert CA, Darrow MC, Naismith JH & Grange M. Cryo-plasma FIB/SEM volume imaging of biological specimens. bioRxiv (2022). https://doi.org/10.1101/2022.09.21.508877

Improved AlphaFold modeling with implicit experimental information

The authors describe a method to improve AlphaFold protein structure prediction by iteratively incorporating experimentally determined cryo-EM density maps. This approach could yield a structural model that is more accurate than what can be obtained using either technique on its own.

 

Terwilliger, T.C., Poon, B.K., Afonine, P.V. et al. Improved AlphaFold modeling with implicit experimental information. Nat Methods 19, 1376–1382 (2022). https://doi.org/10.1038/s41592-022-01645-6

From structure to sequence: antibody discovery using cryo-EM

The authors describe a method to determine monoclonal antibody sequences directly from cryo-electron microscopy-based polyclonal epitope mapping (cryoEMPEM), by combining electron microscopy with next-generation sequencing (NGS).

 

Aleksandar A, Bowman Charles A, Kirchdoerfer Robert N. et al. From structure to sequence: Antibody discovery using cryoEM. Science Advances 8 : eabk2039 (2022). https://doi.org/10.1126/sciadv.abk2039

Structure determination of inactive-state GPCRs with a universal nanobody

 

Here researchers overcome the challenges of obtaining cryo-EM structures of inactive-state GPCRs by using a single-chain camelid antibody (nanobody) yielding resolutions that can exceed those obtained by X-ray crystallography.

 

Robertson, M.J., Papasergi-Scott, M.M., He, F. et al. Structure determination of inactive-state GPCRs with a universal nanobody. Nat Struct Mol Biol (2022). https://doi.org/10.1038/s41594-022-00859-8 (the preprint can be accessed here: https://doi.org/10.1101/2021.11.02.466983)

Cryo-EM applications

A DNA origami rotary ratchet motor

Using DNA origami, the authors built a rotary ratchet motor at the nanoscale whose mechanical capabilities approach those of molecular motors found in cells. They used single particle cryo-EM to validate the 3D structure of the motor's components.

 

Pumm, AK., Engelen, W., Kopperger, E. et al. A DNA origami rotary ratchet motor. Nature 607, 492–498 (2022). https://doi.org/10.1038/s41586-022-04910-y

Structural basis for mismatch surveillance by CRISPR-Cas9

In this paper, the authors used single particle cryo-EM to determine conformational intermediates of Cas9 during mismatch cleavage. Their findings support the rational redesign of high fidelity Cas9 variants in the future.

 

Bravo, J.P.K., Liu, MS., Hibshman, G.N. et al. Structural basis for mismatch surveillance by CRISPR–Cas9. Nature 603, 343–347 (2022). https://doi.org/10.1038/s41586-022-04470-1

Architecture and self-assembly of the jumbo bacteriophage nuclear shell

Laughlin et al., combine cryo-electron tomography and single particle analysis to describe the molecular architecture of jumbo bacteriophage nuclear shell formation.

 

Laughlin, T.G., Deep, A., Prichard, A.M. et al. Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Nature 608, 429–435 (2022). https://doi.org/10.1038/s41586-022-05013-4

Visualizing translation dynamics at atomic detail inside a bacterial cell

The authors leverage in-situ cryo-ET and advanced image-processing algorithms to determine 13 states of translating ribosomes inside a prokaryotic minimal cell model.

 

Xue, L., Lenz, S., Zimmermann-Kogadeeva, M. et al. Visualizing translation dynamics at atomic detail inside a bacterial cell. Nature 610, 205–211 (2022). https://doi.org/10.1038/s41586-022-05255-2

A wheat resistosome defines common principles of immune receptor channels

In this publication, the authors report the first cryo-electron microscopy structure of a wheat immune receptor with its fungus-derived effector. Their data indicate the evolutionary conservation of the corresponding receptor family in plants and enables the structure-guided breeding of wheat species that are more resistant against plant diseases.

 

Förderer, A., Li, E., Lawson, A.W. et al. A wheat resistosome defines common principles of immune receptor channels. Nature 610, 532–539 (2022). https://doi.org/10.1038/s41586-022-05231-w

BacPROTACs mediate targeted protein degradation in bacteria

The authors developed small-molecule degraders in bacteria, so-called BacPROTACs, that could provide a novel way to fight bacterial infections. Single particle cryo-EM was used to visualize the bacterial protease complex in the course of degrading a BacPROTAC-tethered substrate.

 

Morreale FE, Kleine S, Leodolter J. et al. BacPROTACs mediate targeted protein degradation in bacteria. Cell 185, P2338-2353 (2022). https://doi.org/10.1016/j.cell.2022.05.009

Assembly of recombinant tau into filaments identical to those of Alzheimer’s disease and chronic traumatic encephalopathy

 

The authors provide in-vitro assembly conditions for recombinant tau filaments that mimic disease-relevant tau folds as determined by ex-situ cryo-EM. A total of 76 in vitro amyloid structures were determined using single particle cryo-EM for this paper, providing a database of structural model systems for future tauopathy research.

 

Lövestam S, Koh FA, van Knippenberg B, Kotecha A. et al. Assembly of recombinant tau into filaments identical to those of Alzheimer’s disease and chronic traumatic encephalopathy. eLife 11 : e76494 (2022). https://doi.org/10.7554/eLife.76494

The trispecific DARPin ensovibep inhibits diverse SARS-CoV-2 variants

Using single particle cryo-EM, the authors demonstrate how a clinical candidate DARPin antiviral binds the spike protein of diverse SARS-CoV-2 variants to inhibit infection.

 

Rothenberger, S., Hurdiss, D.L., Walser, M. et al. The trispecific DARPin ensovibep inhibits diverse SARS-CoV-2 variants. Nat Biotechnol (2022). https://doi.org/10.1038/s41587-022-01382-3

For Research Use Only. Not for use in diagnostic procedures.