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Beton JG, Mulvaney T, Cragnolini T, Topf M. Cryo-EM structure and B-factor refinement with ensemble representation. Nat Commun 2024; 15:444. [PMID: 38200043 PMCID: PMC10781738 DOI: 10.1038/s41467-023-44593-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
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.
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Affiliation(s)
- Joseph G Beton
- Leibniz Institute of Virology (LIV) and Universitätsklinikum Hamburg Eppendorf (UKE), Centre for Structural Systems Biology (CSSB), 22607, Hamburg, Germany
| | - Thomas Mulvaney
- Leibniz Institute of Virology (LIV) and Universitätsklinikum Hamburg Eppendorf (UKE), Centre for Structural Systems Biology (CSSB), 22607, Hamburg, Germany
| | - Tristan Cragnolini
- 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
| | - Maya Topf
- Leibniz Institute of Virology (LIV) and Universitätsklinikum Hamburg Eppendorf (UKE), Centre for Structural Systems Biology (CSSB), 22607, Hamburg, Germany.
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Mulvaney T, Kretsch RC, Elliott L, Beton JG, Kryshtafovych A, Rigden DJ, Das R, Topf M. CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps. Proteins 2023; 91:1935-1951. [PMID: 37994556 PMCID: PMC10697286 DOI: 10.1002/prot.26644] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/25/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
CASP assessments primarily rely on comparing predicted coordinates with experimental reference structures. However, experimental structures by their nature are only models themselves-their construction involves a certain degree of subjectivity in interpreting density maps and translating them to atomic coordinates. Here, we directly utilized density maps to evaluate the predictions by employing a method for ranking the quality of protein chain predictions based on their fit into the experimental density. The fit-based ranking was found to correlate well with the CASP assessment scores. Overall, the evaluation against the density map indicated that the models are of high accuracy, and occasionally even better than the reference structure in some regions of the model. Local assessment of predicted side chains in a 1.52 Å resolution map showed that side-chains are sometimes poorly positioned. Additionally, the top 118 predictions associated with 9 protein target reference structures were selected for automated refinement, in addition to the top 40 predictions for 11 RNA targets. For both proteins and RNA, the refinement of CASP15 predictions resulted in structures that are close to the reference target structure. This refinement was successful despite large conformational changes often being required, showing that predictions from CASP-assessed methods could serve as a good starting point for building atomic models in cryo-EM maps for both proteins and RNA. Loop modeling continued to pose a challenge for predictors, and together with the lack of consensus amongst models in these regions suggests that modeling, in combination with model-fit to the density, holds the potential for identifying more flexible regions within the structure.
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Affiliation(s)
- Thomas Mulvaney
- Centre for Structural Systems Biology (CSSB), Leibniz-Institut für Virologie (LIV), Hamburg, Germany
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Rachael C Kretsch
- Biophysics Program, Stanford University School of Medicine, California, USA
| | - Luc Elliott
- Institute of Systems, Molecular & Integrative Biology, The University of Liverpool, Liverpool, UK
| | - Joseph G Beton
- Centre for Structural Systems Biology (CSSB), Leibniz-Institut für Virologie (LIV), Hamburg, Germany
| | | | - Daniel J Rigden
- Institute of Systems, Molecular & Integrative Biology, The University of Liverpool, Liverpool, UK
| | - Rhiju Das
- Biophysics Program, Stanford University School of Medicine, California, USA
- Department of Biochemistry, Stanford University School of Medicine, California, USA
- Howard Hughes Medical Institute, Stanford University, California, USA
| | - Maya Topf
- Centre for Structural Systems Biology (CSSB), Leibniz-Institut für Virologie (LIV), Hamburg, Germany
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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