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Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density

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RNA Structure and Dynamics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2568))

Abstract

RNA three-dimensional structures provide rich and vital information for understanding their functions. Recent advances in cryogenic electron microscopy (cryo-EM) allow structure determination of RNAs and ribonucleoprotein (RNP) complexes. However, limited global and local resolutions of RNA cryo-EM maps pose great challenges in tracing RNA coordinates. The Rosetta-based “auto-DRRAFTER” method builds RNA models into moderate-resolution RNA cryo-EM density as part of the Ribosolve pipeline. Here, we describe a step-by-step protocol for auto-DRRAFTER using a glycine riboswitch from Fusobacterium nucleatum as an example. Successful implementation of this protocol allows automated RNA modeling into RNA cryo-EM density, accelerating our understanding of RNA structure–function relationships. Input and output files are being made available at https://github.com/auto-DRRAFTER/springer-chapter.

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Acknowledgments

Computational tasks were performed on SKLB Duyu high performance computing center in Sichuan University and Sherlock 2.0 high performance computing cluster in Stanford University. This work was supported by Ministry of Science and Technology of China (MoST) 2021YFA1301900, Natural Science Foundation of China (NSFC) 82041016 and 32070049, and Sichuan University start-up funding 20822041D4057 to Z.S., the National Science Foundation (NSF) Graduate Research Fellowship award DGE-1656518 to R.R., the Gerald J. Lieberman Fellowship to R.R., the Rosetta REU NSF award 1950697 to P.P., and the National Institutes of Health R35 grant GM122579 to P.P. and R.D.

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Authors and Affiliations

  1. The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China

    Haiyun Ma, Bingnan Luo & Zhaoming Su

  2. Biophysics Program, Stanford University, Stanford, CA, USA

    Phillip Pham, Ramya Rangan, Kalli Kappel & Rhiju Das

Authors
  1. Haiyun Ma
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  2. Phillip Pham
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  3. Bingnan Luo
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  4. Ramya Rangan
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  5. Kalli Kappel
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  6. Zhaoming Su
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  7. Rhiju Das
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Corresponding authors

Correspondence to Zhaoming Su or Rhiju Das .

Editor information

Editors and Affiliations

  1. Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA

    Jienyu Ding

  2. Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA

    Jason R. Stagno

  3. Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA

    Yun-Xing Wang

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© 2023 This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply

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Ma, H. et al. (2023). Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density. In: Ding, J., Stagno, J.R., Wang, YX. (eds) RNA Structure and Dynamics. Methods in Molecular Biology, vol 2568. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2687-0_13

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  • DOI: https://doi.org/10.1007/978-1-0716-2687-0_13

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2686-3

  • Online ISBN: 978-1-0716-2687-0

  • eBook Packages: Springer Protocols

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