A 3D cellular context for the macromolecular world

Abstract

We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community.

Figure 1

The HSV life cycle studied at different length scales. An integrated approach combining high-resolution structure determination methods and CLEM, SXT, 3D EM and ET makes it possible to study dynamic processes at different levels of resolution and complexity, ultimately leading to a better understanding of those processes. Figure and legend adapted from Zeev-Ben-Mordehai et al. under the terms of the CC BY 3.0 license.

Figure 2

Mock-up of what a volume browser for 3D cellular imaging data could look like, using HIV and simian immunodeficiency virus (SIV) as an example, by integrating data from different imaging modalities. The three leftmost images are derived from a 3D-SEM reconstruction and show HIV virion reservoirs in infected macrophages (images adapted from ref. under the terms of the CC BY 2.5 license). These three orthogonal cross-sections and the cube help users orient themselves in the data. The central panel shows a slice from an ET reconstruction in which the features of individual SIV virus particles can be identified. (Image adapted from ref. . This research was originally published in J. Biol. Chem. Bennett, A. et al. Cryoelectron tomographic analysis of an HIV-neutralizing protein and its complex with native viral gp120. J. Biol. Chem. 2007; 282:27754-27759. © the American Society for Biochemistry and Molecular Biology.) Here, biologically meaningful segmentations have been colored and overlaid on the tomogram, and the corresponding annotations are shown at top right. Bottom right shows a 3D rendering of data from the EMDB and PDB (image adapted from ref. , Nature Publishing Group). Figure and legend adapted from ref. under the terms of the CC BY 2.0 UK license.