Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome
- University of California, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, United States
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.
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nucleosome with doubly bound SNF2hEMDataBank, EMD-9353.
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Nucleosome with singly bound SNF2h after motion correctionElectron Microscopy Public Image Archive, EMPIAR-341.
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Cryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.4 AProtein Data Bank, 6NE3.
Article and author information
Author details
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.
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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