Building bridges between cellular and molecular structural biology
- European Bioinformatics Institute, United Kingdom
- FEI Company, France
- University of Helsinki, Finland
- Francis Crick Institute, United Kingdom
- University of Dundee, United Kingdom
- University of Oxford, United Kingdom
- Diamond Light Source Ltd, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, United Kingdom
- London Research Institute, United Kingdom
- Leiden University Medical Center, Netherlands
- Lilly UK, United Kingdom
- The State University of New Jersey, United States
- University of Colorado, United States
- Kitware, Inc., United States
- The Francis Crick Institute, United Kingdom
- Janelia Research Campus, Howard Hughes Medical Institute, United States
- Birkbeck College, United Kingdom
- University of Vic - Central University of Catalonia, Spain
- National Cancer Institute, United States
- Science and Technology Facilities Council, United Kingdom
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.
Article and author information
Author details
Funding
Medical Research Council (MR/L007835)
- Gerard J Kleywegt
European Commission (284209)
- Gerard J Kleywegt
Wellcome (104948)
- Gerard J Kleywegt
National Institutes of Health (R01 GM079429)
- Gerard J Kleywegt
Medical Research Council (MR/N009614/1)
- Martyn Winn
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Werner Kühlbrandt, Max Planck Institute of Biophysics, Germany
Publication history
- Received: February 8, 2017
- Accepted: June 30, 2017
- Accepted Manuscript published: July 6, 2017 (version 1)
- Version of Record published: July 24, 2017 (version 2)
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
Metrics
-
- 3,176
- Page views
-
- 571
- Downloads
-
- 12
- Citations
Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Building bridges between cellular and molecular structural biology
eLife 6:e25835.
https://doi.org/10.7554/eLife.25835
Further reading
-
- Cell Biology
- Structural Biology and Molecular Biophysics
Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and cellular background (Lucas et al., 2021; Lucas et al., 2022). Here, we show that once localized, these particles may be averaged together to generate high-resolution 3D reconstructions. However, regions included in the template may suffer from template bias, leading to inflated resolution estimates and making the interpretation of high-resolution features unreliable. We evaluate conditions that minimize template bias while retaining the benefits of high-precision localization, and we show that molecular features not present in the template can be reconstructed at high resolution from targets found by 2DTM, extending prior work at low-resolution. Moreover, we present a quantitative metric for template bias to aid the interpretation of 3D reconstructions calculated with particles localized using high-resolution templates and fine angular sampling.
-
- Plant Biology
- Structural Biology and Molecular Biophysics
To fire action-potential-like electrical signals, the vacuole membrane requires the two-pore channel TPC1, formerly called SV channel. The TPC1/SV channel functions as a depolarization-stimulated, non-selective cation channel that is inhibited by luminal Ca2+. In our search for species-dependent functional TPC1 channel variants with different luminal Ca2+ sensitivity, we found in total three acidic residues present in Ca2+ sensor sites 2 and 3 of the Ca2+-sensitive AtTPC1 channel from Arabidopsis thaliana that were neutral in its Vicia faba ortholog and also in those of many other Fabaceae. When expressed in the Arabidopsis AtTPC1-loss-of-function background, wild-type VfTPC1 was hypersensitive to vacuole depolarization and only weakly sensitive to blocking luminal Ca2+. When AtTPC1 was mutated for these VfTPC1-homologous polymorphic residues, two neutral substitutions in Ca2+ sensor site 3 alone were already sufficient for the Arabidopsis At-VfTPC1 channel mutant to gain VfTPC1-like voltage and luminal Ca2+ sensitivity that together rendered vacuoles hyperexcitable. Thus, natural TPC1 channel variants exist in plant families which may fine-tune vacuole excitability and adapt it to environmental settings of the particular ecological niche.
