Three-dimensional transmission electron microscopy (3DEM) is emerging as a powerful method for determining the three-dimensional structures of large biological assemblies in solution and in the cell, enabling elucidation of complex biological interactions that are integral to understanding the inner workings of cellular machinery, and yielding novel insights into fundamental biological processes. Hundreds of 3DEM experiments are now reported in the literature each year and more than 1,300 structures are available in public archives through EMDataBank (EMDataBank.org). The major goal of this project is to establish methods to assess the reliability of these structures and to create uniform standards for data exchange, in order to bridge the current substantial gap between 3DEM and established structure determination methods (X-ray crystallography and NMR) in the ability to evaluate and interpret the experimental results. EMDataBank will take a leadership role in facilitating the processes necessary to assess, establish, and disseminate validation methods and data standards. The approach will leverage the expertise and experience of the EMDataBank team in validation, standards, and 3DEM methods development. Validation methods for both 3DEM maps and map-derived models will be established using our own test data sets and software packages as well as those contributed by other electron microscopists. Our results will be made publicly available for comment and review on the EMDataBank website. The PDB exchange dictionary will be extended to support 3DEM community-reviewed validation procedures. Map and map-derived model validation procedures developed through this project will be integrated into the deposition and annotation pipeline of the Protein Data Bank. The work is expected to have a strong transformative impact on both the 3DEM and the wider bioscience communities, enabling independent assessment and interpretation of 3DEM experimental results by both expert and non-expert scientists, and leading to higher reliability and improved consistency of 3DEM structure data.

Public Health Relevance

Three-dimensional transmission electron microscopy (3DEM) is an emerging powerful method for elucidating complex biological interactions that are integral to understanding the inner workings of cellular machinery, and yielding novel insights into fundamental biological processes. The EMDataBank project team will work to establish methods to assess the quality and accuracy of structures determined using 3DEM and to create uniform standards for data exchange, improving the reliability and consistency of data produced by this method.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM079429-07
Application #
8663286
Study Section
Special Emphasis Panel (ZRG1-BCMB-B (02))
Program Officer
Flicker, Paula F
Project Start
2007-08-15
Project End
2017-05-31
Budget Start
2014-06-01
Budget End
2015-05-31
Support Year
7
Fiscal Year
2014
Total Cost
$895,202
Indirect Cost
$117,847
Name
Baylor College of Medicine
Department
Biochemistry
Type
Schools of Medicine
DUNS #
051113330
City
Houston
State
TX
Country
United States
Zip Code
77030
Patwardhan, Ardan (2017) Trends in the Electron Microscopy Data Bank (EMDB). Acta Crystallogr D Struct Biol 73:503-508
Gore, Swanand; Sanz García, Eduardo; Hendrickx, Pieter M S et al. (2017) Validation of Structures in the Protein Data Bank. Structure 25:1916-1927
Dou, Hang; Burrows, Derek W; Baker, Matthew L et al. (2017) Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences. Biophys J 112:2479-2493
Hryc, Corey F; Chen, Dong-Hua; Afonine, Pavel V et al. (2017) Accurate model annotation of a near-atomic resolution cryo-EM map. Proc Natl Acad Sci U S A 114:3103-3108
Young, Jasmine Y; Westbrook, John D; Feng, Zukang et al. (2017) OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. Structure 25:536-545
Yi, Ping; Wang, Zhao; Feng, Qin et al. (2017) Structural and Functional Impacts of ER Coactivator Sequential Recruitment. Mol Cell 67:733-743.e4
Wang, Zhao; Fan, Guizhen; Hryc, Corey F et al. (2017) An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump. Elife 6:
Berman, Helen M; Burley, Stephen K; Kleywegt, Gerard J et al. (2016) The archiving and dissemination of biological structure data. Curr Opin Struct Biol 40:17-22
Salavert-Torres, José; Iudin, Andrii; Lagerstedt, Ingvar et al. (2016) Web-based volume slicer for 3D electron-microscopy data from EMDB. J Struct Biol 194:164-70
DiMaio, F; Chiu, W (2016) Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps. Methods Enzymol 579:255-76

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