Leibniz Institute of Virology (LIV) and Universitätsklinikum Hamburg Eppendorf (UKE), Centre for Structural Systems Biology (CSSB), 22607, Hamburg, Germany.
Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK.
Nat Commun. 2024 Jan 10;15(1):444. doi: 10.1038/s41467-023-44593-1.
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.
冷冻电镜实验产生的大分子组装体的图像被组合以产生三维密度图。通常，将组成分子的原子模型拟合到这些图谱中，然后进行密度引导的精修。我们引入了 TEMPy-ReFF，这是一种在冷冻电镜密度图中进行原子结构精修的方法。我们的方法将原子位置表示为高斯混合模型的分量，利用它们的方差作为 B 因子，用于推导出一个集合描述。我们在一个由 EMDB 中来自 229 个冷冻电镜图谱的大量数据集上进行了广泛测试，分辨率范围从 2.1-4.9 Å，对应于 PDB 和 CERES 原子模型，我们的结果表明，TEMPy-ReFF 集合提供了对冷冻电镜图谱的更好表示。在单模型基础上，它的性能与 CERES 重新精修协议相似，尽管在某些情况下，它提供了更好的图谱拟合。此外，我们的方法能够创建无边界伪影的复合图谱。TEMPy-ReFF 对于更好地解释柔性结构很有用，例如涉及 RNA、DNA 或配体的结构。
