Building bridges between cellular and molecular structural biology

Abstract

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

Keywords: biophysics; computational biology; electron microscopy; emdb; empiar; none; ontology; segmentation; structural biology; systems biology; tomography.

Figure 1.. Segmentation of Plasmodium falciparum–infected erythrocytes.

Soft X-ray tomography shows loss of mechanical integrity of the red cell membrane in the final stages of egress. Panels A-C depict schizonts treated with a selective malarial cGMP-dependent protein kinase G inhibitor (C2), and panels D-F depict schizonts treated with a broad-spectrum cysteine protease inhibitor, E64, which allows parasitophorous vacuole membrane (PVM) rupture but prevents erythrocyte membrane rupture, resulting in merozoites trapped in the blood cell. (A) Slice from tomogram of C2-arrested schizont. (B) Outlines of erythrocyte membrane (red), PVM (yellow), and parasites (cyan) in the tomogram slice in A. (C) 3D rendering of the schizont. The vacuole (yellow) is densely packed with merozoites (cyan) that have been collectively rather than individually rendered, for clarity. The overall height of the cell is ∼5 μm. (D) Tomogram slice from an E64-arrested schizont, shown with outlining of membranes in E. Remnants of the PVM are visible. (F) 3D rendering of the schizont. Figure and legend adapted with permission from Hale et al. (2017). Scale bar 1 μm. DOI: http://dx.doi.org/10.7554/eLife.25835.002

Figure 2.. Arrangement of Lassa virus glycoprotein spikes on the virion surface.

Left to right: A slice from a tomographic volume of Lassa viruses, a sub-tomogram average of the glycoprotein spike, and the sub-tomogram average inserted back onto a virus reconstruction. Images adapted from Li et al., 2016 (under a CC BY 4.0 license). DOI: http://dx.doi.org/10.7554/eLife.25835.003

Figure 3.. Mock-up of a possible Segmentation-Annotation Tool (SAT).

Image slices are shown with the segmentations overlaid. (A) The top right panel presents a tree that enables the user to select the segment to be annotated, and existing annotations are shown in the middle right panel. The bottom right panel provides pre-defined lists of annotation terms for frequently studied assemblies and complexes. The image in the left panel is adapted from Müller et al. (2014) (under a CC BY 3.0 license). (B) The top right and middle right panels are similar to those in A. The bottom right panel provides a search option to find relevant terms. The image in the left panel is adapted from Santarella-Mellwig et al., 2013 (under a CC BY 4.0 license). DOI: http://dx.doi.org/10.7554/eLife.25835.004

Figure 4.. Segmentation-annotation workflow.

A user launches the Segmentation-Annotation Tool and uploads segmentations obtained with third-party software. After the segmentation has been annotated with biologically meaningful terms, a segmentation file is written in EMDB-SFF format; this file can be uploaded to the Electron Microscopy Data Bank when the structure is deposited. Once released, the EMDB-SFF file can be used for the integration of structural data between different imaging scales and across resources. The Volume browser mock-up (bottom right) contains images adapted from Bennett et al. (2007) and Bennett et al. (2009) (under a CC0 1.0 license). The 3D rendering was generated from EMDB entry EMD-5020 and PDB entry 3dno (Liu et al., 2008). DOI: http://dx.doi.org/10.7554/eLife.25835.005