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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...

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Updated: Dec 12, 2025

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM

Biao Zhang¹, Xi Zhang², Robin Pearce²

¹Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

Journal of Molecular Biology

|August 11, 2020

Summary

A new protocol combines I-TASSER protein structure prediction with cryo-electron microscopy (cryo-EM) density map fitting. This method successfully generates accurate atomic models from low-resolution maps, advancing structural biology.

Keywords:

Cryo-EM protein structure prediction replica-exchange Monte Carlo simulation structure and density-map fitting structure refinement

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Last Updated: Dec 12, 2025

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Single Particle Cryo-Electron Microscopy: From Sample to Structure

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Published on: May 29, 2021

Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction

Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction

Published on: January 9, 2015

Area of Science:

Structural Biology
Biophysics
Computational Biology

Background:

Cryo-electron microscopy (cryo-EM) is rapidly advancing, creating a need for methods to build atomic models from low-resolution density maps.
Accurate atomic models are crucial for understanding protein function and biological mechanisms.

Purpose of the Study:

To develop and validate a robust protocol for generating and refining atomic-level structural models from low-resolution cryo-EM density maps.
To enable structure modeling directly from amino acid sequences using cryo-EM data.

Main Methods:

A novel pipeline integrating I-TASSER protein structure prediction with cryo-EM density map-based fitting.
Utilizing rigid-body fitting, flexible fragment adjustment, and atomic-level refinement simulations.
Testing the protocol on a diverse set of 285 non-homologous proteins.

Main Results:

The protocol generated correct protein folds for 260 out of 285 proteins.
28% of the generated models achieved root-mean-square deviations (RMSDs) below 2 Ångstroms.
Model quality strongly correlated with the accuracy of initial I-TASSER predictions, particularly concerning the template modeling score (TM-score).

Conclusions:

The proposed pipeline offers a unified approach for structure prediction and refinement guided by cryo-EM density maps.
This method is suitable for large-scale structure modeling and refinement, especially from low-to-medium resolution data.
The findings highlight the importance of initial model quality for successful cryo-EM-based structure determination.