- EMDB-41227: Cryo-electron tomography reconstruction of 80S ribosome in Transl... -
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Entry
Database: EMDB / ID: EMD-41227
Title
Cryo-electron tomography reconstruction of 80S ribosome in Translocation-intermediate-POST-3 state class 5, obtained from the EMPIAR-10987 dataset by constrained 3D classification.
Map data
Sample
Complex: 80S ribosome in Translocation-intermediate-POST-3 state class 5
Keywords
ribosome / 80S / non-rotated / cryo-ET
Biological species
Mus musculus (house mouse)
Method
subtomogram averaging / cryo EM / Resolution: 10.9 Å
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01GM141223
United States
Chan Zuckerberg Initiative
Visual Proteomics Imaging
United States
Citation
Journal: Nat Methods / Year: 2023 Title: nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography. Authors: Hsuan-Fu Liu / Ye Zhou / Qinwen Huang / Jonathan Piland / Weisheng Jin / Justin Mandel / Xiaochen Du / Jeffrey Martin / Alberto Bartesaghi / Abstract: Single-particle cryo-electron tomography is an emerging technique capable of determining the structure of proteins imaged within the native context of cells at molecular resolution. While high- ...Single-particle cryo-electron tomography is an emerging technique capable of determining the structure of proteins imaged within the native context of cells at molecular resolution. While high-throughput techniques for sample preparation and tilt-series acquisition are beginning to provide sufficient data to allow structural studies of proteins at physiological concentrations, the complex data analysis pipeline and the demanding storage and computational requirements pose major barriers for the development and broader adoption of this technology. Here, we present a scalable, end-to-end framework for single-particle cryo-electron tomography data analysis from on-the-fly pre-processing of tilt series to high-resolution refinement and classification, which allows efficient analysis and visualization of datasets with hundreds of tilt series and hundreds of thousands of particles. We validate our approach using in vitro and cellular datasets, demonstrating its effectiveness at achieving high-resolution and revealing conformational heterogeneity in situ. The framework is made available through an intuitive and easy-to-use computer application, nextPYP ( http://nextpyp.app ).
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