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Cited by 63Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and FunctionMicrotubule and mitosis dynamics

A microtubule RELION-based pipeline for cryo-EM image processing

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Cook, Alexander D., Manka, Szymon W., Wang, Su, Moores, Carolyn A., Atherton, Joseph·2020·Journal of Structural Biology
DOI 10.1016/j.jsb.2019.10.004PMC PMC6961209

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Abstract

Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views owing to the high structural similarity of α- and β-tubulin. The determination of the αβ-tubulin register and seam location during image processing is essential for alignment accuracy that enables determination of biologically relevant structures. Here we present a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing near-atomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins.

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  • The 13-protofilament assignment of the initial average was confirmed by overlaying and cross-correlating it with the six references (11-16 protofilaments) from the Microtubule RELION-based Pipeline (MiRP).

    “This was confirmed by overlaying and cross-correlating the average with the six references (11–16 PFs) from the Microtubule RELION-based Pipeline (MiRP) (Cook et al., 2020).”

    From StableMARK-decorated microtubules in cells have expanded lattices (2025) · cites this paper as Cook et al., 2020

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Cited by

Sorted by citations

Authors
Cook, A. D., Manka, S. W., Wang, S., Moores, C. A., & Atherton, J.
Affiliations
Institute of Structural and Molecular Biology (GB)
Corresponding author
Atherton, Joseph
ORCID
Venue
Journal of Structural Biology
Publisher
Elsevier BV
Published
2020-01
Volume
209
Issue
1
Pages
107402
ISSN
1047-8477 (ISSN-L)
DOI
10.1016/j.jsb.2019.10.004
PMC
PMC6961209
OpenAlex
W2980132977
Cited by
63
References
2
Citations by year
2026: 9 · 2025: 15 · 2024: 10 · 2023: 9 · 2022: 12 · 2021: 3 · 2020: 4 · 2019: 1
FWCI
2.50
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Structural Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • BIROn (Birkbeck, University of London) (acceptedVersion)
Funders
  • Medical Research Council (MR/R000352/1)
  • Wellcome Trust (079605/Z/06/Z, 101488/Z/13/Z)
  • BBSRC (BB/L014211/1)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
Keywords
microtubules, αβ-tubulin, RELION, high-resolution reconstruction, binding proteins
MeSH terms
Humans, Image Processing, Computer-Assisted, Microtubule-Associated Proteins, Microtubules, Databases, Factual, Cryoelectron Microscopy

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