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Structure paper

TitleCryo-EM structure of SWI/SNF complex bound to a nucleosome.
Journal, issue, pagesNature, Vol. 579, Issue 7799, Page 452-455, Year 2020
Publish dateMar 11, 2020
AuthorsYan Han / Alexis A Reyes / Sara Malik / Yuan He /
PubMed AbstractThe chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair. It hydrolyses ATP to remodel ...The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair. It hydrolyses ATP to remodel chromatin structure by sliding and evicting histone octamers, creating DNA regions that become accessible to other essential factors. However, our mechanistic understanding of the remodelling activity is hindered by the lack of a high-resolution structure of complexes from this family. Here we report the cryo-electron microscopy structure of Saccharomyces cerevisiae SWI/SNF bound to a nucleosome, at near-atomic resolution. In the structure, the actin-related protein (Arp) module is sandwiched between the ATPase and the rest of the complex, with the Snf2 helicase-SANT associated (HSA) domain connecting all modules. The body contains an assembly scaffold composed of conserved subunits Snf12 (also known as SMARCD or BAF60), Snf5 (also known as SMARCB1, BAF47 or INI1) and an asymmetric dimer of Swi3 (also known as SMARCC, BAF155 or BAF170). Another conserved subunit, Swi1 (also known as ARID1 or BAF250), resides in the core of SWI/SNF, acting as a molecular hub. We also observed interactions between Snf5 and the histones at the acidic patch, which could serve as an anchor during active DNA translocation. Our structure enables us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and to propose a model for how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation.
External linksNature / PubMed:32188938 / PubMed Central
MethodsEM (single particle)
Resolution4.7 - 10.0 Å
Structure data

20933

6uxv

EMDB-20933, PDB-6uxv:
SWI/SNF Body Module
Method: EM (single particle) / Resolution: 4.7 Å

20934

6uxw

EMDB-20934, PDB-6uxw:
SWI/SNF nucleosome complex with ADP-BeFx
Method: EM (single particle) / Resolution: 8.96 Å

EMDB-20935:
SWI/SNF nucleosome complex with ATP-gamma-S
Method: EM (single particle) / Resolution: 10.0 Å

Chemicals

ChemComp-PO4:
PHOSPHATE ION / Phosphate

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

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • saccharomyces cerevisiae s288c (yeast)
  • Saccharomyces cerevisiae (brewer's yeast)
  • xenopus laevis (African clawed frog)
  • synthetic construct (others)
KeywordsTRANSCRIPTION / SWI/SNF / chromatin remodeler / TRANSCRIPTION/DNA / TRANSCRIPTION-DNA complex

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