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Structure paper

TitleMechanism of DNA translocation underlying chromatin remodelling by Snf2.
Journal, issue, pagesNature, Vol. 567, Issue 7748, Page 409-413, Year 2019
Publish dateMar 13, 2019
AuthorsMeijing Li / Xian Xia / Yuanyuan Tian / Qi Jia / Xiaoyu Liu / Ying Lu / Ming Li / Xueming Li / Zhucheng Chen /
PubMed AbstractChromatin remodellers include diverse enzymes with distinct biological functions, but nucleosome-sliding activity appears to be a common theme. Among the remodelling enzymes, Snf2 serves as the ...Chromatin remodellers include diverse enzymes with distinct biological functions, but nucleosome-sliding activity appears to be a common theme. Among the remodelling enzymes, Snf2 serves as the prototype to study the action of this protein family. Snf2 and related enzymes share two conserved RecA-like lobes, which by themselves are able to couple ATP hydrolysis to chromatin remodelling. The mechanism by which these enzymes couple ATP hydrolysis to translocate the nucleosome along the DNA remains unclear. Here we report the structures of Saccharomyces cerevisiae Snf2 bound to the nucleosome in the presence of ADP and ADP-BeF. Snf2 in the ADP-bound state adopts an open conformation similar to that in the apo state, and induces a one-base-pair DNA bulge at superhelix location 2 (SHL2), with the tracking strand showing greater distortion than the guide strand. The DNA distortion propagates to the proximal end, leading to staggered translocation of the two strands. The binding of ADP-BeF triggers a closed conformation of the enzyme, resetting the nucleosome to a relaxed state. Snf2 shows altered interactions with the DNA in different nucleotide states, providing the structural basis for DNA translocation. Together, our findings suggest a fundamental mechanism for the DNA translocation that underlies chromatin remodelling.
External linksNature / PubMed:30867599
MethodsEM (single particle)
Resolution3.47 - 4.31 Å
Structure data

6879

5z3l

EMDB-6879, PDB-5z3l:
Structure of Snf2-nucleosome complex in apo state
Method: EM (single particle) / Resolution: 4.31 Å

6880

5z3o

EMDB-6880, PDB-5z3o:
Structure of Snf2-nucleosome complex in ADP state
Method: EM (single particle) / Resolution: 3.62 Å

6882

5z3u

EMDB-6882, PDB-5z3u:
Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state
Method: EM (single particle) / Resolution: 4.31 Å

6883

5z3v

EMDB-6883, PDB-5z3v:
Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state
Method: EM (single particle) / Resolution: 4.22 Å

9748

6iy2

EMDB-9748, PDB-6iy2:
Structure of Snf2-MMTV-A nucleosome complex at shl2 in ADP state
Method: EM (single particle) / Resolution: 3.47 Å

9749

6iy3

EMDB-9749, PDB-6iy3:
Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state
Method: EM (single particle) / Resolution: 3.67 Å

Chemicals

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

ChemComp-MG:
Unknown entry

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Source
  • xenopus laevis (African clawed frog)
  • saccharomyces cerevisiae (brewer's yeast)
  • synthetic construct (others)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • mus musculus (house mouse)
  • Saccharomyces cerevisiae S288c (yeast)
KeywordsSTRUCTURAL PROTEIN/HYDROLASE/DNA / complex / nucleosome / chromatin remodeling / gene regulation / STRUCTURAL PROTEIN-HYDROLASE-DNA complex / DNA BINDING PROTEIN / NUCLEAR PROTEIN

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