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Structure paper

TitleStructures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling.
Journal, issue, pagesNat Struct Mol Biol, Vol. 26, Issue 4, Page 258-266, Year 2019
Publish dateMar 13, 2019
AuthorsLijuan Yan / Hao Wu / Xuemei Li / Ning Gao / Zhucheng Chen /
PubMed AbstractChromatin remodelers are diverse enzymes, and different models have been proposed to explain how these proteins work. Here we report the 3.3 Å-resolution cryogenic electron microscopy (cryo-EM) ...Chromatin remodelers are diverse enzymes, and different models have been proposed to explain how these proteins work. Here we report the 3.3 Å-resolution cryogenic electron microscopy (cryo-EM) structures of Saccharomyces cerevisiae ISWI (ISW1) in complex with the nucleosome in adenosine diphosphate (ADP)-bound and ADP-BeF-bound states. The data show that after nucleosome binding, ISW1 is activated by substantial rearrangement of the catalytic domains, with the regulatory AutoN domain packing the first RecA-like core and the NegC domain being disordered. The high-resolution structure reveals local DNA distortion and translocation induced by ISW1 in the ADP-bound state, which is essentially identical to that induced by the Snf2 chromatin remodeler, suggesting a common mechanism of DNA translocation. The histone core remains largely unperturbed, and prevention of histone distortion by crosslinking did not inhibit the activity of yeast ISW1 or its human homolog. Together, our findings suggest a general mechanism of chromatin remodeling involving local DNA distortion without notable histone deformation.
External linksNat Struct Mol Biol / PubMed:30872815
MethodsEM (single particle)
Resolution3.37 - 3.87 Å
Structure data

9718

6jyl

EMDB-9718, PDB-6jyl:
The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state
Method: EM (single particle) / Resolution: 3.37 Å

9719

6k1p

EMDB-9719, PDB-6k1p:
The complex of ISWI-nucleosome in the ADP.BeF-bound state
Method: EM (single particle) / Resolution: 3.87 Å

9720

6iro

EMDB-9720, PDB-6iro:
the crosslinked complex of ISWI-nucleosome in the ADP-bound state
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-MG:
Unknown entry

Source
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • xenopus laevis (African clawed frog)
  • escherichia coli k-12 (bacteria)
KeywordsDNA BINDING PROTEIN/DNA / chromatin remodelling / single particle CryO-EM / nucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

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