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Related Concept Videos

Cryo-electron Microscopy01:28

Cryo-electron Microscopy

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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...
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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.
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Related Experiment Video

Updated: Dec 28, 2025

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion
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Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps.

Agnel Praveen Joseph1, Ingvar Lagerstedt2, Arjen Jakobi3

  • 1Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom.

Journal of Chemical Information and Modeling
|February 12, 2020
PubMed
Summary
This summary is machine-generated.

This study introduces a new method to compare cryo-electron microscopy (cryo-EM) maps, revealing structural differences in macromolecular assemblies. The tool aids in identifying conformational changes and evaluating atomic model accuracy.

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Area of Science:

  • Structural biology
  • Biophysics
  • Biochemistry

Background:

  • Cryo-electron microscopy (cryo-EM) is crucial for determining macromolecular structures.
  • Advancements in cryo-EM enable higher resolution, facilitating atomic model building.
  • Interpreting complex datasets often requires comparing different structural states or models.

Purpose of the Study:

  • To develop a robust method for calculating differences between cryo-EM maps and/or fitted atomic models.
  • To provide a user-friendly tool for visualizing and analyzing structural variations.
  • To enhance the interpretation of cryo-EM data, particularly for conformational and compositional changes.

Main Methods:

  • A novel approach for map comparison using amplitude matching in resolution shells.
  • Inclusion of local amplitude scaling to address variations in local resolution.
  • Implementation as a user-friendly tool within the CCP-EM software package.
  • Development of a processing protocol for clean and interpretable difference maps.

Main Results:

  • The method effectively calculates differences between cryo-EM maps and atomic models.
  • Local amplitude scaling successfully accounts for local resolution variations.
  • Demonstrated utility in identifying conformational and compositional differences, including ligand binding.
  • Difference maps proved valuable for assessing atomic model fit to cryo-EM data.

Conclusions:

  • The developed method provides a reliable way to analyze structural differences from cryo-EM data.
  • The CCP-EM tool facilitates the interpretation of macromolecular assembly dynamics and composition.
  • This approach enhances the accuracy and utility of cryo-EM in structural biology research.