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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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Related Experiment Video

Updated: Jul 4, 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

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model.

Xiao Wang¹, Han Zhu¹, Genki Terashi²

¹Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907, USA.

Biorxiv : the Preprint Server for Biology

|February 8, 2024

Summary

This summary is machine-generated.

DiffModeler, an automated method, accurately models complex protein structures from intermediate-resolution cryo-electron microscopy (cryo-EM) maps. It integrates diffusion models and AlphaFold2 predictions, achieving high accuracy even for large complexes.

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Last Updated: Jul 4, 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

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

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
Computational biology
Biophysics

Background:

Cryo-electron microscopy (cryo-EM) is crucial for determining multi-chain protein complex structures.
Modeling protein complexes at intermediate resolutions (5-10 Å) remains a significant challenge.
Existing methods struggle with accurate structure fitting and de novo modeling in this resolution range.

Approach:

Introduces DiffModeler, a fully automated method for protein complex structure modeling.
Employs a diffusion model for backbone tracing.
Integrates AlphaFold2-predicted single-chain structures for enhanced structure fitting.

Key Points:

DiffModeler achieves exceptional accuracy on intermediate-resolution cryo-EM maps, with an average TM-Score of 0.92.
Successfully modeled a 47-chain, 13,462-residue complex with a TM-Score of 0.94.
Demonstrates versatility at low resolutions (10-20 Å) and excels in protein-nucleic acid complex modeling with CryoREAD.

Conclusions:

DiffModeler significantly advances automated protein complex structure modeling, especially at intermediate resolutions.
Provides a robust solution for challenging cryo-EM data.
Shows potential for modeling large, complex biological assemblies and nucleic acid interactions.