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Related Concept Videos

Cryo-electron Microscopy01:28

Cryo-electron Microscopy

4.5K
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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Preparation of Samples for Electron Microscopy01:20

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To be visualized by an electron microscope, either transmission or scanning, biological samples need to be fixed (stabilized) so the electron beam does not destroy them and dried thoroughly (desiccated/dehydrated) so the vacuum does not affect them. Fixation needs to be done as quickly as possible because the sample properties will start changing as soon as it is removed from its natural environment. For example, in a tissue sample, the oxygen levels begin decreasing, causing an altered...
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Related Experiment Video

Updated: Mar 15, 2026

Routine Collection of High-Resolution cryo-EM Datasets Using 200 KV Transmission Electron Microscope
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Routine Collection of High-Resolution cryo-EM Datasets Using 200 KV Transmission Electron Microscope

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Databases and Archiving for CryoEM.

A Patwardhan1, C L Lawson2

  • 1Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom.

Methods in Enzymology
|August 31, 2016
PubMed
Summary
This summary is machine-generated.

Three public archives (EMDB, PDB, EMPIAR) support structural biology by archiving cryo-electron microscopy (cryo-EM) data. These resources ensure data accessibility for reuse, reassessment, and integration, crucial for advancing biological research.

Keywords:
DatabasesEMDBEMDataBankEMPIARProtein Data BankValidation

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Area of Science:

  • Structural Biology
  • Biophysics
  • Bioinformatics

Background:

  • Three public archives—EMDB, PDB, and EMPIAR—serve the cryo-electron microscopy (cryo-EM) field.
  • These archives are essential for data accessibility, reuse, and integration within structural and bioinformatics research.
  • Journal mandates for data deposition underscore the importance of these public archives.

Purpose of the Study:

  • To describe the current state of public archives for cryo-EM data.
  • To outline resources for data deposition, access, searching, visualization, and validation.
  • To discuss ongoing initiatives, opportunities, and future challenges for these archives.

Main Methods:

  • Review of existing public archives (EMDB, PDB, EMPIAR) for cryo-EM data.
  • Description of data deposition, access, and validation resources.
  • Analysis of current trends and future prospects in structural biology data archiving.

Main Results:

  • Cryo-EM data archiving is managed by EMDB (reconstructions), PDB (models), and EMPIAR (raw images).
  • These archives facilitate data reuse, reassessment, and integration, supported by journal publication mandates.
  • The field is rapidly evolving with high-resolution structures and electron tomography, necessitating archive adaptation.

Conclusions:

  • Public archives are critical infrastructure for structural biology, enabling data sharing and reproducibility.
  • Ongoing evolution of archives is necessary to keep pace with technological advancements like electron tomography.
  • Addressing future challenges will ensure continued support for the structural biology community.