2024
DOI: 10.1101/2024.04.26.591129
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An image processing pipeline for electron cryo-tomography in RELION-5

Alister Burt,
Bogdan Toader,
Rangana Warshamanage
et al.

Abstract: Electron tomography of frozen, hydrated samples allows structure determination of macro-molecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three-dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for de novo atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and … Show more

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Cited by 10 publications
(5 citation statements)
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“…We processed the MscS2Δ2–29 cryo-EM data with Relion version 3.1 [ 53 ], 4.0 [ 54 ] and 5.0 beta [ 55 ]. Movie alignment, drift correction, and dose weighing were performed using MotionCor2 [ 56 ], and CTF estimation was done with CTFFIND (v4.1.14) [ 57 ].…”
Section: Methodsmentioning
confidence: 99%
“…We processed the MscS2Δ2–29 cryo-EM data with Relion version 3.1 [ 53 ], 4.0 [ 54 ] and 5.0 beta [ 55 ]. Movie alignment, drift correction, and dose weighing were performed using MotionCor2 [ 56 ], and CTF estimation was done with CTFFIND (v4.1.14) [ 57 ].…”
Section: Methodsmentioning
confidence: 99%
“…Downstream subtomogram averaging (STA) (Galaz-Montoya and Ludtke, 2017;Förster, 2022) can yield structures at subnanometer (Schur et al, 2013) and near-atomic (Schur et al, 2016) resolutions, even for complexes within cells (Tegunov et al, 2021). While STA was first demonstrated nearly 30 years ago (Walz et al, 1997) using ad hoc scripts (Nicastro et al, 2006), the first semi-automated pipelines for STA started emerging only about a decade ago (Hrabe et al, 2012;Castaño-Díez et al, 2012;Galaz-Montoya et al, 2015), and have become increasingly sophisticated and efficient (Galaz-Montoya et al, 2016;Bharat and Scheres, 2016;Castaño-Díez et al, 2017;Himes and Zhang, 2018;Fernandez and Li, 2021;Zivanov et al, 2022;Burt et al, 2024), with the field rapidly taking large strides towards full automation for some specimens (Chen et al, 2019;Ni et al, 2022;Balyschew et al, 2023). Clearly, these advancements have positioned STA at the forefront of high-resolution structural biology in situ.…”
Section: Cryogenic Em/et and Fib-sem At The Dawn Of High-resolution C...mentioning
confidence: 99%
“…In the sharpened map the DNA density was absent. Particles from the non-uniform refinement were transferred to RELION v. 5.0-beta (12) for DNA-focused refinement. After 3D refinement in RELION, signal from the protein was subtracted, the particles were re-centered on DNA, and five DNA volume classes were reconstructed.…”
Section: Cryo-em Data Processingmentioning
confidence: 99%