SNAP output for PDB entry 6ne3 [SNAP web server]

PDB-id

6ne3; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein-DNA

Method

cryo-EM (3.9 Å)

Summary

cryo-EM structure of singly-bound snf2h-nucleosome complex with snf2h bound at shl-2

Reference

Armache JP, Gamarra N, Johnson SL, Leonard JD, Wu S, Narlikar GJ, Cheng Y (2019): "Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome." Elife, 8. doi: 10.7554/eLife.46057.

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-BeF_x that capture two potential 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 2 bp translocation. FRET studies indicate that ADP-BeF_x 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.