Data management challenges in three-dimensional EM

Abstract

This report describes the outcomes of the Data Management Challenges in 3D Electron Microscopy workshop. Key topics discussed include data models, validation and raw-data archiving. The meeting participants agreed that the EMDataBank should take the lead in addressing these issues, and concrete action points were agreed upon that will have a substantial impact on the accessibility of three-dimensional EM data in biology and medicine.

Figure 1

Trends in 3DEM. The cumulative number of released maps in the EMDB and 3DEM-derived models in the PDB are shown as a function of time.

Figure 2

Holdings of the EMDB by 3DEM technique. A representative example of each category is shown: single particle, human αβ-crystallin 24-mer (EMD-1894, PDB 2YGD); icosahedral, cytoplasmic polyhedrosis virus (EMD-5256, PDB 3IZX); helical, GMPPCP-stabilized human dynamin 1 ΔPRD polymer (EMD-1949, PDB 3ZYS); tomogram or subtomogram average, radial spokes from Chlamydomonas reinhardtii flagella (EMD-1941); 2D crystal, pig gastric H⁺,K⁺-ATPase with bound BeF and SCH28080 (EMD-1831, PDB 2XZB).

Figure 3

Visual analysis of EMDB entries. Visual analysis page for EMDB entry EMD-1831 (http://pdbe.org/emd-1831/analysis), the structure of pig gastric H⁺,K⁺-ATPase with bound BeF and SCH28080 (ref. 24). The top right panel presents orthogonal surface projections of the map. The bottom right panel displays orthogonal surface projections of the map overlaid with the fitted PDB model 2XZB (green, all atoms; blue, backbone only). The chart on the top left shows the histogram of density values, and the one below shows the fraction of model atoms contained in the map as a function of contour level (red line, recommended level).