Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Structural Topology-based Electrostatic Model (STEM) Reveals Ion-Coordination Exchange as a Driver of RNA Folding Dynamics.

bioRxiv : the preprint server for biology·2026

Same author

Cryo-EM structure of the naked mole-rat ribosome reveals a stabilized split 28S rRNA.

Nature communications·2026

Same author

Covalent Organic Frameworks with Intrinsic Pendant Aldehydes for Efficient Nitrate Electroreduction.

Small (Weinheim an der Bergstrasse, Germany)·2026

Same author

Exploring functional transitions of the 2'-dG riboswitch aptamer.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Cleavage region organizes the structural architecture of the SINE-derived B2 repressive ribozyme.

Communications biology·2026

Same author

Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.

Nucleic acids research·2026

Search research articles

Related Experiment Video

Updated: Apr 10, 2026

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

Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions.

Serdal Kirmizialtin¹, Justus Loerke², Elmar Behrmann³

¹Department of Chemistry, New York University, Abu Dhabi, United Arab Emirates; New Mexico Consortium, Los Alamos, New Mexico, USA; Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.

Methods in Enzymology

|June 13, 2015

Summary

This study introduces an automated method for building atomic models from high-resolution cryo-electron microscopy (cryo-EM) data. The new technique uses molecular dynamics to create accurate ribosome structures, streamlining structural biology research.

Keywords:

High-resolution cryo-EM Molecular modeling Molecular simulation RNA structure Ribosome cryo-EM cryo-EM fitting

More Related Videos

Cryo-EM and Single-Particle Analysis with Scipion

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

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

Related Experiment Videos

Last Updated: Apr 10, 2026

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

Cryo-EM and Single-Particle Analysis with Scipion

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

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

Area of Science:

Structural Biology
Biophysics
Computational Biology

Background:

High-resolution cryo-electron microscopy (cryo-EM) generates vast datasets for ribosomes.
Current modeling methods for high-resolution cryo-EM often require manual intervention and crystallographic techniques.
Developing automated methods is crucial for efficiently analyzing the increasing volume of cryo-EM data.

Purpose of the Study:

To present an automated fitting technique for high-resolution cryo-EM data.
To generate all-atom models that are highly consistent with cryo-EM electron density.
To improve the efficiency and accuracy of structural model generation for large biomolecular complexes.

Main Methods:

Utilized a molecular dynamics approach to optimize atomic positions.
Incorporated a potential function including cross-correlation with EM density and stereochemical preservation.
Employed a hybrid structure-based/ab initio molecular dynamics potential and simulated annealing integration.

Main Results:

Successfully generated atomistic models of the human ribosome.
Achieved models consistent with high-resolution cryo-EM reconstructions.
Demonstrated improved performance using simulated annealing integration compared to standard molecular dynamics.

Conclusions:

The developed automated method effectively produces accurate all-atom models from high-resolution cryo-EM data.
This technique has the potential to simultaneously model numerous ribosome complexes, facilitating large-scale structural studies.
Automated modeling can significantly accelerate the process of structural determination in cryo-EM.