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. 2013 Nov;184(2):173-81.
doi: 10.1016/j.jsb.2013.09.021. Epub 2013 Oct 7.

Web-based Visualisation and Analysis of 3D Electron-Microscopy Data From EMDB and PDB

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Free PMC article

Web-based Visualisation and Analysis of 3D Electron-Microscopy Data From EMDB and PDB

Ingvar Lagerstedt et al. J Struct Biol. .
Free PMC article

Abstract

The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed.

Keywords: 3DEM; EM VTC; EMDB; Electron Microscopy Data Bank; Electron Microscopy Validation Task Force; Electron microscopy; Electron tomography; FSC; Fourier Shell Correlation; Macromolecular structure; OAV; OME; OME Remote Objects; OMERO; Open Astex Viewer; Open Microscopy Environment; PDB; PDBe; Protein Data Bank; Protein Data Bank in Europe; Three-Dimensional Electron Microscopy; Visualisation; Worldwide Protein Data Bank; wwPDB.

Figures

Fig.1
Fig.1
Interactive viewers for 3DEM data in EMDB and PDB. (a) Volume viewer showing EMD-5591 (80S D. melanogaster ribosome) and PDB entries 3j38, 3j39, 3j3c and 3j3e (Anger et al., 2013). The viewer contains the EM volume and a trace representation of the fitted models. (b) Slice viewer with EMD-1906 (tomogram of thylakoid membranes from spinach chloroplasts). The slice viewer only displays one plane at a time, which avoids the need to down-sample the map.
Fig.2
Fig.2
Effect of down-sampling. Comparing a deposited map with the down-sampled map used by the volume viewer. Most of the secondary structure detail remains, but side-chain density evident in the original map is lost in the down-sampled map. The 3.3 Å resolution map is of a helical reconstruction of Tobacco Mosaic Virus, EMD-5185 (Ge and Zhou, 2011) with fitted PDB model 3j06 (chain A, residue 41–58 shown here). (a) Detail of deposited map, 512 × 512 × 512 voxels. (b) Detail of map down-sampled to 160 × 160 × 160 voxels. The surface is rendered at a lower density level, 3.7, than the recommended level used for the deposited map, 6.42; this is done to give the volumes similar visual appearance.
Fig.3
Fig.3
Visual analysis page components (see main text for further details). (a) View along the X-axis of EMD-1836, adeno-associated virus type 1 (Gerlach et al., 2011). The visual analysis pages also include views along the Y and Z axes. (b) View along X-axis of EMD-1831 with fitted PDB entry 2xzb, pig gastric H,K-ATPase (Abe et al., 2011). Backbone atoms are shown in blue, side-chain atoms in green. (c) View along the Z-axis of EMD-1273, the immunological synapse between a cytotoxic T lymphocyte and a target cell (Stinchcombe et al., 2006). The blue object is a segmentation of the synaptic cleft provided by the depositors. (d) Map-density plot for EMD-1916, T. thermophilus ribosome recycling factor (Yokoyama et al., 2012). The spike at zero density indicates that the volume has been masked prior to deposition. (e) Enclosed map-volume plot for EMD-2168, S. cerevisiae 60S ribosomal subunit in complex with Rei1 (Greber et al., 2012). The volume of the map is plotted as a function of contour level. The graph and the two lines intersect in one point, suggesting that the contour level results in a map whose volume is consistent with the value estimated from the molecular weight of the specimen. This is one of the better examples in EMDB and more commonly the lines do not intersect in one point. (f) FSC curve for EMD-5357, bacteriophage phi6 procapsid (Nemecek et al., 2011). (g) Fractional atom inclusion as a function of contour level for PDB entry 4a7f fitted to EMD-1987, F-actin-myo1E-tropomyosin complex (Behrmann et al., 2012). Separate curves are shown for trace/backbone atoms only (blue) and all atoms (green). (h) Atom inclusion by residue for PDB entry 3j3f fitted to EMD-5592, human 60S rRNA (Anger et al., 2013). The colour-ramping indicates the extent to which the atoms of a residue are inside or outside the map, with green indicating 100% inside, and red 100% outside the map. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig.3
Fig.3
Visual analysis page components (see main text for further details). (a) View along the X-axis of EMD-1836, adeno-associated virus type 1 (Gerlach et al., 2011). The visual analysis pages also include views along the Y and Z axes. (b) View along X-axis of EMD-1831 with fitted PDB entry 2xzb, pig gastric H,K-ATPase (Abe et al., 2011). Backbone atoms are shown in blue, side-chain atoms in green. (c) View along the Z-axis of EMD-1273, the immunological synapse between a cytotoxic T lymphocyte and a target cell (Stinchcombe et al., 2006). The blue object is a segmentation of the synaptic cleft provided by the depositors. (d) Map-density plot for EMD-1916, T. thermophilus ribosome recycling factor (Yokoyama et al., 2012). The spike at zero density indicates that the volume has been masked prior to deposition. (e) Enclosed map-volume plot for EMD-2168, S. cerevisiae 60S ribosomal subunit in complex with Rei1 (Greber et al., 2012). The volume of the map is plotted as a function of contour level. The graph and the two lines intersect in one point, suggesting that the contour level results in a map whose volume is consistent with the value estimated from the molecular weight of the specimen. This is one of the better examples in EMDB and more commonly the lines do not intersect in one point. (f) FSC curve for EMD-5357, bacteriophage phi6 procapsid (Nemecek et al., 2011). (g) Fractional atom inclusion as a function of contour level for PDB entry 4a7f fitted to EMD-1987, F-actin-myo1E-tropomyosin complex (Behrmann et al., 2012). Separate curves are shown for trace/backbone atoms only (blue) and all atoms (green). (h) Atom inclusion by residue for PDB entry 3j3f fitted to EMD-5592, human 60S rRNA (Anger et al., 2013). The colour-ramping indicates the extent to which the atoms of a residue are inside or outside the map, with green indicating 100% inside, and red 100% outside the map. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

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