1. Structural Biology and Molecular Biophysics
  2. Computational and Systems Biology
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Cutting Edge: Building bridges between cellular and molecular structural biology

  1. Ardan Patwardhan  Is a corresponding author
  2. Robert Brandt
  3. Sarah J Butcher
  4. Lucy Collinson
  5. David Gault
  6. Kay Grünewald
  7. Corey Hecksel
  8. Juha T Huiskonen
  9. Andrii Iudin
  10. Martin L Jones
  11. Paul K Korir
  12. Abraham J Koster
  13. Ingvar Lagerstedt
  14. Catherine L Lawson
  15. David Mastronarde
  16. Matthew McCormick
  17. Helen Parkinson
  18. Peter B Rosenthal
  19. Stephan Saalfeld
  20. Helen R Saibil
  21. Sirarat Sarntivijai
  22. Irene Solanes Valero
  23. Sriram Subramaniam
  24. Jason R Swedlow
  25. Ilinca Tudose
  26. Martyn Winn
  27. Gerard J Kleywegt  Is a corresponding author
  1. European Molecular Biology Laboratory, European Bioinformatics Institute, United Kingdom
  2. FEI, France
  3. University of Helsinki, Finland
  4. Francis Crick Institute, United Kingdom
  5. University of Dundee, United Kingdom
  6. University of Oxford, United Kingdom
  7. Baylor College of Medicine, United States
  8. Leiden University Medical Center, The Netherlands
  9. Rutgers, The State University of New Jersey, United States
  10. University of Colorado, United States
  11. Kitware, Inc., United States
  12. Howard Hughes Medical Institute, United States
  13. Birkbeck College, United Kingdom
  14. National Cancer Institute, United States
  15. Science and Technology Facilities Council, United Kingdom
Feature Article
Cite this article as: eLife 2017;6:e25835 doi: 10.7554/eLife.25835
4 figures

Figures

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.

https://doi.org/10.7554/eLife.25835.002
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).

https://doi.org/10.7554/eLife.25835.003
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).

https://doi.org/10.7554/eLife.25835.004
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).

https://doi.org/10.7554/eLife.25835.005

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