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A flexible framework for multi-particle refinement in cryo-electron tomography

DOI: 10.1371/journal.pbio.3001319 DOI Help

Authors: Alister Burt (Université Grenoble Alpes, CEA, CNRS, IBS) , Lorenzo Gaifas (Université Grenoble Alpes, CEA, CNRS, IBS) , Tom Dendooven (MRC Laboratory of Molecular Biology) , Irina Gutsche (Université Grenoble Alpes, CEA, CNRS, IBS)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Plos Biology , VOL 19

State: Published (Approved)
Published: August 2021

Open Access Open Access

Abstract: Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) are increasingly used for macromolecular structure determination in situ. Here, we introduce a set of computational tools and resources designed to enable flexible approaches to STA through increased automation and simplified metadata handling. We create a bidirectional interface between the Dynamo software package and the Warp-Relion-M pipeline, providing a framework for ab initio and geometrical approaches to multiparticle refinement in M. We illustrate the power of working within this framework by applying it to EMPIAR-10164, a publicly available dataset containing immature HIV-1 virus-like particles (VLPs), and a challenging in situ dataset containing chemosensory arrays in bacterial minicells. Additionally, we provide a comprehensive, step-by-step guide to obtaining a 3.4-Å reconstruction from EMPIAR-10164. The guide is hosted on https://teamtomo.org/, a collaborative online platform we establish for sharing knowledge about cryo-ET.

Journal Keywords: Metadata; Preprocessing; Tomography; Software tools; Data processing; Ecosystems; Optimization; HIV-1

Subject Areas: Information and Communication Technology, Biology and Bio-materials

Diamond Offline Facilities: Electron Bio-Imaging Centre (eBIC)
Instruments: Scios-Scios at Diamond

Added On: 31/08/2021 10:41

Documents:
journal.pbio.3001319.pdf

Discipline Tags:

Computing & software technologies Information & Communication Technologies Structural biology Data processing Life Sciences & Biotech

Technical Tags:

Imaging Tomography Cryo Electron Tomography (Cryo ET)