PXD025287

PXD025287 is an original dataset announced via ProteomeXchange.

Title	Nucleosome recognition and DNA distortion by the Chd1 remodeler revealed at 2.6 Å resolution
Description	Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. The Chd1 remodeler specializes in shifting nucleosomes into evenly spaced arrays, a defining characteristic of chromatin in gene bodies that blocks spurious transcription initiation. Linked to some forms of autism and commonly mutated in prostate cancer, Chd1 is essential for maintaining pluripotency in stem cells. Here we report a complex of yeast Chd1 bound to a nucleosome in a nucleotide-free state, determined by cryo-electron microscopy (cryo-EM) to 2.6 Å resolution. The structure shows a bulge of the DNA tracking strand where the ATPase motor engages the nucleosome, consistent with an initial stage in DNA translocation. Unlike other remodeler-nucleosome complexes, nucleosomal DNA compensates for the remodeler-induced bulge with a bulge of the complementary DNA strand one helical turn downstream from the ATPase motor. Unexpectedly, the structure also reveals an N-terminal binding motif, called ChEx, which binds on the exit-side acidic patch of the nucleosome. The ChEx motif can displace a LANA-based peptide from the acidic patch, which suggests a means by which Chd1 remodelers may block competing chromatin remodelers from acting on the opposite side of the nucleosome.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:52:53.526.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stephen Fried
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-08 19:47:07	ID requested
1	2022-02-23 12:19:55	announced
⏵ 2	2023-11-14 08:52:54	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Chd1,Nucleosome, XL-MS, chromatin remodeler

Stephen Fried
contact affiliation	Stephen Fried Johns Hopkins University Fried Lab Chemistry Department
contact email	sdfried@jhu.edu
lab head
Stephen Fried
contact affiliation	Johns Hopkins University
contact email	sdfried@jhu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD025287
     1. Label: PRIDE project
     2. Name: Nucleosome recognition and DNA distortion by the Chd1 remodeler revealed at 2.6 Å resolution