ENaC

EMDB: Electron Microscopy Data Bank

The Electron Microscopy Data Bank (EMDB) is a public repository for the deposition and retrieval of three-dimensional electron microscopy (3D-EM) density maps. It is an essential resource for the structural biology community, providing access to data that supports the understanding of the molecular architecture of biological macromolecules.

History

The EMDB was established in 2002 at the European Bioinformatics Institute (EBI) in collaboration with the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI). The creation of the EMDB was driven by the increasing use of electron microscopy in structural biology and the need for a centralized repository for 3D-EM data.

Purpose and Scope

The primary purpose of the EMDB is to provide a freely accessible archive of 3D-EM density maps and associated metadata. These maps are derived from various electron microscopy techniques, including single-particle analysis, electron tomography, and electron crystallography. The EMDB supports the deposition of maps from both cryo-electron microscopy (cryo-EM) and negative stain electron microscopy.

Data Deposition and Access

Researchers can deposit their 3D-EM maps into the EMDB through a structured submission process. Each deposition is assigned a unique accession code, which can be used to retrieve the data. The EMDB provides tools for searching and visualizing the deposited maps, allowing users to explore the structural details of macromolecular complexes.

Integration with Other Databases

The EMDB is closely integrated with the Protein Data Bank (PDB), which archives atomic models of macromolecules. Many EMDB entries are linked to corresponding PDB entries, providing a comprehensive view of both the density maps and the atomic models derived from them. This integration facilitates the study of structure-function relationships in biological systems.

Technological Advances

Recent advances in electron microscopy technology, such as the development of direct electron detectors and improved image processing algorithms, have significantly enhanced the resolution and quality of 3D-EM maps. These improvements have led to a rapid increase in the number of high-resolution structures deposited in the EMDB.

Impact on Structural Biology

The EMDB has had a profound impact on the field of structural biology by enabling the visualization of large macromolecular assemblies that are difficult to study using other techniques. It has contributed to numerous discoveries in areas such as virology, enzymology, and membrane protein biology.

Also see

• Protein Data Bank (PDB)
• Cryo-electron microscopy
• Structural biology
• Macromolecular complex