SNAP output for PDB entry 7tn2 [SNAP web server]

PDB-id

7tn2; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein

Method

cryo-EM (2.3 Å)

Summary

Composite model of a chd1-nucleosome complex in the nucleotide-free state derived from 2.3a and 2.7a cryo-EM maps

Reference

Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP (2022): "Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state." Nat.Struct.Mol.Biol., 29, 121-129. doi: 10.1038/s41594-021-00719-x.

Abstract

Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. Here we report a complex of the Chd1 remodeler bound to a nucleosome in a nucleotide-free state, determined by cryo-EM to 2.3 Å resolution. The remodeler stimulates the nucleosome to absorb an additional nucleotide on each strand at two different locations: on the tracking strand within the ATPase binding site and on the guide strand one helical turn from the ATPase motor. Remarkably, the additional nucleotide on the tracking strand is associated with a local transformation toward an A-form geometry, explaining how sequential ratcheting of each DNA strand occurs. The structure also reveals a histone-binding motif, ChEx, which can block opposing remodelers on the nucleosome and may allow Chd1 to participate in histone reorganization during transcription.