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TitleNucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state.
Journal, issue, pagesNat Struct Mol Biol, Vol. 29, Issue 2, Page 121-129, Year 2022
Publish dateFeb 16, 2022
AuthorsIlana M Nodelman / Sayan Das / Anneliese M Faustino / Stephen D Fried / Gregory D Bowman / Jean-Paul Armache /
PubMed AbstractChromatin 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 ...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.
External linksNat Struct Mol Biol / PubMed:35173352 / PubMed Central
MethodsEM (single particle)
Resolution2.3 - 2.9 Å
Structure data

25479

7swy

7tn2

EMDB-25479: 2.3 A structure of the ATP-dependent chromatin remodeler Chd1 bound to the nucleosome in a nucleotide-free state
PDB-7swy: 2.6 A structure of a 40-601[TA-rich+1]-40 nucleosome
PDB-7tn2: Composite model of a Chd1-nucleosome complex in the nucleotide-free state derived from 2.3A and 2.7A Cryo-EM maps
Method: EM (single particle) / Resolution: 2.3 Å

EMDB-25480:
2.7 A structure of the ATP-dependent chromatin remodeler Chd1 bound to the nucleosome in a nucleotide-free state. This entry contains a better resolved DNA-binding domain
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-25481:
2.6 A structure of the nucleosome from a class without Chd1
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-25483:
2.9 A structure of the nucleosome-bound ChEx, part of the chromatin remodeler Chd1
Method: EM (single particle) / Resolution: 2.9 Å

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • xenopus laevis (African clawed frog)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN/DNA / CHD1 / chromatin remodeling / ATPase / DBD / nucleosome / remodeling / transcription / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

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