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    Cryo-EM structure and B-factor refinement with ensemble representation

    Mulvaney, Tom and Beton, Joseph and Cragnolini, Tristan and Topf, Maya (2024) Cryo-EM structure and B-factor refinement with ensemble representation. Nature Communications 15 (444), ISSN 2041-1723.

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    Abstract

    Cryo-EM experiments produce images of macromolecular assemblies that are combined to produce three-dimensional density maps. Typically, atomic models of the constituent molecules are fitted into these maps, followed by a density-guided refinement. We introduce TEMPy-ReFF, a method for atomic structure refinement in cryo-EM density maps. Our method represents atomic positions as components of a Gaussian mixture model, utilising their variances as B-factors, which are used to derive an ensemble description. Extensively tested on a substantial dataset of 229 cryo-EM maps from EMDB ranging in resolution from 2.1-4.9 Å with corresponding PDB and CERES atomic models, our results demonstrate that TEMPy-ReFF ensembles provide a superior representation of cryo-EM maps. On a single-model basis, it performs similarly to the CERES re-refinement protocol, although there are cases where it provides a better fit to the map. Furthermore, our method enables the creation of composite maps free of boundary artefacts. TEMPy-ReFF is useful for better interpretation of flexible structures, such as those involving RNA, DNA or ligands.

    Metadata

    Item Type: Article
    School: Birkbeck Faculties and Schools > Faculty of Science > School of Natural Sciences
    Research Centres and Institutes: Structural Molecular Biology, Institute of (ISMB)
    Depositing User: Tristan Cragnolini
    Date Deposited: 22 Feb 2024 14:59
    Last Modified: 22 Feb 2024 15:30
    URI: https://eprints.bbk.ac.uk/id/eprint/52987

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