Abstract

Using a manifold-based analysis of experimental diffraction snapshots from an X-ray free electron laser, we determine the three-dimensional structure and conformational landscape of the PR772 virus to a detector-limited resolution of 9 nm. Our results indicate that a single conformational coordinate controls reorganization of the genome, growth of a tubular structure from a portal vertex and release of the genome. These results demonstrate that single-particle X-ray scattering has the potential to shed light on key biological processes.

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Acknowledgements

We acknowledge valuable discussions with H. Chapman, E. Lattman, J. Spence and I. Vartaniants. The research conducted at University of Wisconsin–Milwaukee was supported by the US Department of Energy, Office of Science, Basic Energy Sciences, under contract DE-SC0002164 (A.O., algorithm design and development) and by the US National Science Foundation (NSF) under contract STC 1231306 (A.O., numerical trial models and data analysis; M.S., data analysis) and under contract number 1551489 (A.O., underlying analytical models). The research at Arizona State University was supported by the NSF under contract STC 1231306 (B.G.H.). Use of the Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under contract DE-AC02-76SF00515.

Author information

Author notes

    • Ahmad Hosseinizadeh
    • , Ghoncheh Mashayekhi
    • , Jeremy Copperman
    • , Peter Schwander
    •  & Abbas Ourmazd

    These authors contributed equally to this work.

Affiliations

  1. Department of Physics, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin, USA.

    • Ahmad Hosseinizadeh
    • , Ghoncheh Mashayekhi
    • , Jeremy Copperman
    • , Peter Schwander
    • , Ali Dashti
    • , Reyhaneh Sepehr
    • , Russell Fung
    • , Marius Schmidt
    •  & Abbas Ourmazd
  2. Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA.

    • Chun Hong Yoon
    •  & Andrew Aquila
  3. Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona, USA.

    • Brenda G Hogue
  4. Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA.

    • Brenda G Hogue
  5. School of Life Sciences, Arizona State University, Tempe, Arizona, USA.

    • Brenda G Hogue
  6. Brookhaven National Laboratory, Upton, New York, USA.

    • Garth J Williams

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Contributions

A.H.: algorithmic design, data preprocessing, single-particle hit finding, orientation and structural recovery, preparation of paper. G.M.: conformational analysis, preparation of paper. J.C.: conformational analysis and validation, preparation of paper. P.S.: experimental and algorithmic design, code development, data preprocessing, data analysis, experiments at LCLS, preparation of paper. A.D., R.S. and R.F.: data-analytical contributions. M.S.: analysis of results, preparation of paper. C.H.Y.: experimental design, data collection. B.G.H.: sample selection, preparation and characterization, experiments at LCLS, preparation of paper. G.J.W.: planning and execution of experiment and discussions of data and analysis. A.A.: experimental design, data collection, preparation of paper. A.O.: experimental and algorithmic design, data analysis and interpretation, preparation of paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Abbas Ourmazd.

Integrated supplementary information

Supplementary information

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    Supplementary Text and Figures

    Supplementary Figures 1–8 and Supplementary Note

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    Life Sciences Reporting Summary

    Life Sciences Reporting Summary

Excel files

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    Supplementary Data

    Single-particle indices

Videos

  1. 1.

    3D conformational movie with imposed icosahedral symmetry.

    Evolution of the 3D structure of the PR772 virus, and the occupancy along the dominant conformational reaction coordinate. These results were obtained assuming icosahedral symmetry.

  2. 2.

    3D conformational movie without imposing icosahedral symmetry.

    Evolution of the 3D structure of the PR772 virus, and the occupancy along the conformational reaction coordinate without imposing icosahedral symmetry. Note the protrusion of a tubular structure, and the concentration of the genome toward the tube.

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DOI

https://doi.org/10.1038/nmeth.4395

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