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M3: an integrative framework for structure determination of molecular machines

Nature Methods volume 14, pages 897902 (2017) | Download Citation

Abstract

We present a broadly applicable, user-friendly protocol that incorporates sparse and hybrid experimental data to calculate quasi-atomic-resolution structures of molecular machines. The protocol uses the HADDOCK framework, accounts for extensive structural rearrangements both at the domain and atomic levels and accepts input from all structural and biochemical experiments whose data can be translated into interatomic distances and/or molecular shapes.

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Acknowledgements

This work was supported by the EMBL, the EU FP7 ITN project RNPnet (contract number 289007) and the DFG grant CA294/3-2. E.K. acknowledges support from the Alexander von Humboldt Foundation through a Humboldt Research Fellowship for Postdoctoral Researchers. We thank J. Kirkpatrick for critical reading of the manuscript and B. Simon for discussion and support with CNS. A.M.J.J.B. acknowledges funding from the European H2020 e-Infrastructure grants West-Life (grant no. 675858) and BioExcel (grant no. 675728).

Author information

Author notes

    • Ezgi Karaca
    •  & João P G L M Rodrigues

    Present addresses: Izmir International Biomedicine and Genome Institute (iBG-izmir), Dokuz Eylül University Saglik Yerleskesi, Izmir, Turkey (E.K.) and Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA (J.P.G.L.M.R.).

Affiliations

  1. European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.

    • Ezgi Karaca
    • , Andrea Graziadei
    •  & Teresa Carlomagno
  2. Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, the Netherlands.

    • João P G L M Rodrigues
    •  & Alexandre M J J Bonvin
  3. Leibniz University Hannover, Centre for Biomolecular Drug Research, Hannover, Germany.

    • Teresa Carlomagno
  4. Helmholtz Centre for Infection Research, Group of Structural Chemistry, Braunschweig, Germany.

    • Teresa Carlomagno

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Contributions

E.K. designed the studies, developed software, performed structure calculations, analyzed and interpreted data and wrote the manuscript, J.P.G.L.M.R. developed software; A.G. analyzed experiments; A.M.J.J.B. provided software and assisted in software development; T.C. designed the studies, assisted in data interpretation, wrote the manuscript and supervised the project.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Teresa Carlomagno.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–7, Supplementary Table 1 and Supplementary Note 1.

  2. 2.

    Life Sciences Reporting Summary

    Life Sciences Reporting Summary.

  3. 3.

    Supplementary Protocol

    M3 manual.

Zip files

  1. 1.

    Supplementary Software

    HADDOCK-M3 software.

  2. 2.

    Supplementary Data

    Restraint files, starting structures and final models.

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DOI

https://doi.org/10.1038/nmeth.4392

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