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. 2011 Jan;39(Database issue):D456-64.
doi: 10.1093/nar/gkq880. Epub 2010 Oct 8.

EMDataBank.org: unified data resource for CryoEM

Catherine L Lawson  1 , Matthew L Baker, Christoph Best, Chunxiao Bi, Matthew Dougherty, Powei Feng, Glen van Ginkel, Batsal Devkota, Ingvar Lagerstedt, Steven J Ludtke, Richard H Newman, Tom J Oldfield, Ian Rees, Gaurav Sahni, Raul Sala, Sameer Velankar, Joe Warren, John D Westbrook, Kim Henrick, Gerard J Kleywegt, Helen M Berman, Wah Chiu
Affiliations

EMDataBank.org: unified data resource for CryoEM

Catherine L Lawson et al. Nucleic Acids Res. 2011 Jan.

Abstract

Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global 'one-stop shop' resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.

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Figures

Figure 1.
Figure 1.
EM entries in EMDB and PDB, cumulative by year (*2010 data is through July).
Figure 2.
Figure 2.
Current distribution of EM map entry types.
Figure 3.
Figure 3.
Image gallery of EM structures in EMDB and PDB (labels are database ids with “EMD-” prefixes omitted for brevity; scaling is arbitrary). Icosahedral—5115: West Nile virus-antibody complex (53); 5131: wild-rabbit hemorrhagic disease virus (54); 5161: Partitivirus (55); 5173: Hepatitis E particles (56); other single particle: 1540: pre-translocational ribosome (57); 1485: DNA ligase–PCNA–DNA complex (58); 1640: yeast V-ATPase (59); 1732: tripeptidyl peptidase II (60); 1734: rubisco-methyltransferase complex (61); 1733: 20S proteasome (62); Helical—1730: tobacco mosaic virus (63); 5136: HIV-1 capsid tubular crystal (64); Tomogram averages—1644: Borrelia flagellar motor (65); 1704: Tula Hantavirus glycoprotein spikes (66); 1707: Podovirus P-SSP7 infecting Prochlorococcus marinus (67); Map+model pairs—1046-1gru: GroES–GroEL complex (68); 1201-2dfs: Myosin V (69); 1340-2p4n: kinesin bound to a microtubule (70); 5037-3fi1: ion-coupled transport protein NhaA (71); 5186-3iyt: apoptosome–procaspase-9 CARD complex (72). All images were created using OpenAstexViewer as implemented on the EMDB atlas pages for these entries.
Figure 4.
Figure 4.
Example EMDB atlas page.
Figure 5.
Figure 5.
Tools for 3D visualization of EM structural data. EM viewer (top left) and OpenAstexViewer (top right) are Java-based 3D viewers that can be launched from the EMDB atlas ‘Visualization’ pages. EM viewer employs a compact single contour-level mesh representation for lightweight map viewing; OpenAstexViewer enables exploration of maps and their fitted models with adjustable map contour level. The EMDataBank.org web service implemented in UCSF chimera (bottom panel) expedites search of the EMDB and subsequent map + model download. The example shown is GroEL [EMD-5001and PDB 3CAU; (73)].
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