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Review
. 2016:579:393-412.
doi: 10.1016/bs.mie.2016.04.015. Epub 2016 Jun 16.

Databases and Archiving for CryoEM

A Patwardhan  1 , C L Lawson  2
Affiliations
Review

Databases and Archiving for CryoEM

A Patwardhan et al. Methods Enzymol. 2016.

Abstract

CryoEM in structural biology is currently served by three public archives-EMDB for 3DEM reconstructions, PDB for models built from 3DEM reconstructions, and EMPIAR for the raw 2D image data used to obtain the 3DEM reconstructions. These archives play a vital role for both the structural community and the wider biological community in making the data accessible so that results may be reused, reassessed, and integrated with other structural and bioinformatics resources. The important role of the archives is underpinned by the fact that many journals mandate the deposition of data to PDB and EMDB on publication. The field is currently undergoing transformative changes where on the one hand high-resolution structures are becoming a routine occurrence while on the other hand electron tomography is enabling the study of macromolecules in the cellular context. Concomitantly the archives are evolving to best serve their stakeholder communities. In this chapter, we describe the current state of the archives, resources available for depositing, accessing, searching, visualizing and validating data, on-going community-wide initiatives and opportunities, and challenges for the future.

Keywords: Databases; EMDB; EMDataBank; EMPIAR; Protein Data Bank; Validation.

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Figures

Figure 1
Figure 1
Released 3DEM entries in EMDB and PDB, cumulative by year, since the start of the EMDataBank Project in 2007.
Figure 2
Figure 2
Trend in reported 3DEM method for EMDB entries released between 2010 and 2015, showing annual releases.
Figure 3
Figure 3
Trend in reported resolution for EMDB entries released between 2010 and 2015, showing annual releases.
Figure 4
Figure 4
Trends in released EMDB entries where a direct electron detector was used. The numbers for 2016 are for the period up to 23/3/2016. a) The column chart shows the total number of entries where a direct electron detector was used (axis to the left) and the line chart shows the fraction of all entries (axis to the right). b) These charts are similar to a) except that the resolution is restricted to 4Å or better.
Figure 4
Figure 4
Trends in released EMDB entries where a direct electron detector was used. The numbers for 2016 are for the period up to 23/3/2016. a) The column chart shows the total number of entries where a direct electron detector was used (axis to the left) and the line chart shows the fraction of all entries (axis to the right). b) These charts are similar to a) except that the resolution is restricted to 4Å or better.
See this image and copyright information in PMC

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