1. Chromosomes and Gene Expression
  2. Structural Biology and Molecular Biophysics

Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

  1. Jean Paul Armache
  2. Nathan Gamarra
  3. Stephanie L Johnson
  4. John D Leonard
  5. Shenping Wu
  6. Geeta J Narlikar  Is a corresponding author
  7. Yifan Cheng  Is a corresponding author
  1. University of California, San Francisco, United States
  2. Howard Hughes Medical Institute, University of California, San Francisco, United States
https://doi.org/10.7554/eLife.46057
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Cite this article
  1. Jean Paul Armache
  2. Nathan Gamarra
  3. Stephanie L Johnson
  4. John D Leonard
  5. Shenping Wu
  6. Geeta J Narlikar
  7. Yifan Cheng
(2019)
Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome
eLife 8:e46057.
https://doi.org/10.7554/eLife.46057
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Abstract

The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeFx that capture two reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, appear disordered. The disordered acidic patch is expected to inhibit the second SNF2h protomer, while disorder near the dyad is expected to promote DNA translocation. The other structure doesn't show octamer deformation, but surprisingly shows a 2bp translocation. FRET studies indicate that ADP-BeFx predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation.

Data availability

The cryo-EM density maps have been deposited in the Electron Microscopy Data Bank (EMDB) under accession numbers EMD-9353 (nucleosome with doubly bound SNF2h), EMD-9351 (nucleosome with singly bound SNF2h at SHL+2, 8.4Å), EMD-9352 (SNF2h-nucleosome, 3.4Å), EMD-9354 (SNF2h-nucleosome SHL-2, 3.9Å), and EMD-9355 (SNF2h-nucleosome SHL+2, 6.9Å) (Figure 2-supplement 4). Corresponding unsharpened map and both half maps were deposited as maps associated with the primary depositions. Particle image stacks of nucleosome with singly bound SNF2h after motion correction have been deposited in the Electron Microscopy Public Image Archive (http://www.ebi.ac.uk/pdbe/emdb/empiar/) under accession number EMPIAR-341. Atomic coordinate of nucleosome with SNF2h bound near entry side has been deposited in the Protein Data Bank (PDB) under the accession number 6NE3.

The following data sets were generated

Article and author information

Author details

  1. Jean Paul Armache

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  2. Nathan Gamarra

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2430-8662

  3. Stephanie L Johnson

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  4. John D Leonard

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    John D Leonard, Is affiliated with 3T Biosciences and has no other competing interests to declare.

  5. Shenping Wu

    Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  6. Geeta J Narlikar

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    For correspondence
    Geeta.Narlikar@ucsf.edu
    Competing interests
    Geeta J Narlikar, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1920-0147

  7. Yifan Cheng

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    For correspondence
    ycheng@ucsf.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9535-0369

Funding

National Institutes of Health (GM073767)

  • Geeta J Narlikar

National Science Foundation

  • Nathan Gamarra

Howard Hughes Medical Institute

  • Yifan Cheng

University of California, San Francisco (Program for Breakthrough Biomedical Research)

  • Yifan Cheng

Leukemia and Lymphoma Society

  • Stephanie L Johnson

National Institutes of Health (GM108455)

  • Geeta J Narlikar

National Institutes of Health (R01GM082893)

  • Yifan Cheng

National Institutes of Health (1S10OD020054)

  • Yifan Cheng

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Sjors HW Scheres, MRC Laboratory of Molecular Biology, United Kingdom

Version history

  1. Received: February 14, 2019
  2. Accepted: June 18, 2019
  3. Accepted Manuscript published: June 18, 2019 (version 1)
  4. Version of Record published: July 5, 2019 (version 2)

Copyright

© 2019, Armache et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Jean Paul Armache
  2. Nathan Gamarra
  3. Stephanie L Johnson
  4. John D Leonard
  5. Shenping Wu
  6. Geeta J Narlikar
  7. Yifan Cheng
(2019)
Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome
eLife 8:e46057.
https://doi.org/10.7554/eLife.46057

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