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All-atom RNA structure determination from cryo-EM maps

Nature Biotechnology (2024)Cite this article

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Abstract

Many methods exist for determining protein structures from cryogenic electron microscopy maps, but this remains challenging for RNA structures. Here we developed EMRNA, a method for accurate, automated determination of full-length all-atom RNA structures from cryogenic electron microscopy maps. EMRNA integrates deep learning-based detection of nucleotides, three-dimensional backbone tracing and scoring with consideration of sequence and secondary structure information, and full-atom construction of the RNA structure. We validated EMRNA on 140 diverse RNA maps ranging from 37 to 423 nt at 2.0–6.0 Å resolutions, and compared EMRNA with auto-DRRAFTER, phenix.map_to_model and CryoREAD on a set of 71 cases. EMRNA achieves a median accuracy of 2.36 Å root mean square deviation and 0.86 TM-score for full-length RNA structures, compared with 6.66 Å and 0.58 for auto-DRRAFTER. EMRNA also obtains a high residue coverage and sequence match of 93.30% and 95.30% in the built models, compared with 58.20% and 42.20% for phenix.map_to_model and 56.45% and 52.3% for CryoREAD. EMRNA is fast and can build an RNA structure of 100 nt within 3 min.

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Fig. 1: Overview of the EMRNA framework.
Fig. 2: Overall performance of EMRNA for top 1, 5 and 10 predictions on the test set of 71 cases.
Fig. 3: Comparison between EMRNA and auto-DRRAFTER in building the full-length RNA structure.
Fig. 4: Comparison of EMRNA, phenix.map_to_model and CryoREAD in recovering RNA fragments on the test set of 71 cases.
Fig. 5: Quality assessment of the built EMRNA models.
Fig. 6: Comparison between EMRNA and CryoREAD on raw RNA-only maps.

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Data availability

The raw data of the evaluation results are provided in the article and supplementary tables. All published data sets used in this paper were taken from the EMDB and PDB (accession codes specified in the figure captions and in supplementary tables). The EMRNA input maps and output models used in the study are available at https://zenodo.org/records/10225107 ref. 67. Source data are provided with this paper.

Code availability

The EMRNA package is freely available for academic or noncommercial users at http://huanglab.phys.hust.edu.cn/EMRNA/ or https://zenodo.org/records/10540040 (ref. 68).

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (grant nos. 32161133002, 62072199 and 32071247) and the startup grant of Huazhong University of Science and Technology. The computation is completed in the HPC Platform of Huazhong University of Science and Technology.

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Authors and Affiliations

  1. School of Physics and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, China

    Tao Li, Jiahua He, Hong Cao, Yi Zhang, Ji Chen, Yi Xiao & Sheng-You Huang

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Contributions

S.-Y.H. and Y.X. conceived and supervised the project. T.L., J.H., H.C., Y.Z. and S.-Y.H. designed and performed the experiments. S.-Y.H. and T.L. analyzed the data. H.C. and J.C. tested the program. T.L. and S.-Y.H. wrote the paper. All authors read and approved the final version of the paper.

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Correspondence to Yi Xiao or Sheng-You Huang.

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Li, T., He, J., Cao, H. et al. All-atom RNA structure determination from cryo-EM maps. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-024-02149-8

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