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Cryo-electron Microscopy

Cryo-electron Microscopy

Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...

Electron Microscope Tomography and Single-particle Reconstruction

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...

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Related Experiment Video

Updated: Jul 6, 2025

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

Published on: January 31, 2022

Cryo-EM structure and B-factor refinement with ensemble representation.

Joseph G Beton¹, Thomas Mulvaney¹, Tristan Cragnolini^1,2

¹Leibniz Institute of Virology (LIV) and Universitätsklinikum Hamburg Eppendorf (UKE), Centre for Structural Systems Biology (CSSB), 22607, Hamburg, Germany.

Nature Communications

|January 10, 2024

Summary

This summary is machine-generated.

We developed TEMPy-ReFF, a new method for refining atomic structures within cryo-electron microscopy (cryo-EM) density maps. This approach enhances the representation of macromolecular assemblies, improving the interpretation of flexible biological structures.

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Last Updated: Jul 6, 2025

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Single Particle Cryo-Electron Microscopy: From Sample to Structure

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Published on: May 29, 2021

Area of Science:

Structural Biology
Biophysics
Computational Biology

Background:

Cryo-electron microscopy (cryo-EM) generates 3D density maps of macromolecular assemblies.
Atomic models are typically fitted and refined into these maps using density-guided methods.

Purpose of the Study:

To introduce TEMPy-ReFF, a novel method for atomic structure refinement in cryo-EM density maps.
To provide a superior representation of cryo-EM maps, especially for flexible structures.

Main Methods:

Atomic positions represented as Gaussian mixture model components.
Utilized variances as B-factors for ensemble description.
Tested on 229 cryo-EM maps (2.1-4.9 Å resolution) with PDB and CERES models.

Main Results:

TEMPy-ReFF ensembles offer a superior representation of cryo-EM maps compared to standard methods.
Single-model performance is comparable to CERES re-refinement, with improved fits in some cases.
Enables creation of composite maps without boundary artifacts.

Conclusions:

TEMPy-ReFF provides an advanced method for atomic structure refinement in cryo-EM.
The ensemble approach improves the interpretation of flexible biological macromolecules like RNA, DNA, and ligands.