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TitleNucleosome flipping drives kinetic proofreading and processivity by SWR1.
Journal, issue, pagesNature, Vol. 636, Issue 8041, Page 251-257, Year 2024
Publish dateNov 6, 2024
AuthorsPaul Girvan / Adam S B Jalal / Elizabeth A McCormack / Michael T Skehan / Carol L Knight / Dale B Wigley / David S Rueda /
PubMed AbstractThe yeast SWR1 complex catalyses the exchange of histone H2A-H2B dimers in nucleosomes, with Htz1-H2B dimers. Here we used single-molecule analysis to demonstrate two-step double exchange of the two ...The yeast SWR1 complex catalyses the exchange of histone H2A-H2B dimers in nucleosomes, with Htz1-H2B dimers. Here we used single-molecule analysis to demonstrate two-step double exchange of the two H2A-H2B dimers in a canonical yeast nucleosome with Htz1-H2B dimers, and showed that double exchange can be processive without release of the nucleosome from the SWR1 complex. Further analysis showed that bound nucleosomes flip between two states, with each presenting a different face, and hence histone dimer, to SWR1. The bound dwell time is longer when an H2A-H2B dimer is presented for exchange than when presented with an Htz1-H2B dimer. A hexasome intermediate in the reaction is bound to the SWR1 complex in a single orientation with the 'empty' site presented for dimer insertion. Cryo-electron microscopy analysis revealed different populations of complexes showing nucleosomes caught 'flipping' between different conformations without release, each placing a different dimer into position for exchange, with the Swc2 subunit having a key role in this process. Together, the data reveal a processive mechanism for double dimer exchange that explains how SWR1 can 'proofread' the dimer identities within nucleosomes.
External linksNature / PubMed:39506114 / PubMed Central
MethodsEM (single particle)
Resolution3.8 - 4.7 Å
Structure data

18471

8qku

EMDB-18471, PDB-8qku:
SWR1-nucleosome complex in configuration 1
Method: EM (single particle) / Resolution: 3.8 Å

18472

8qkv

EMDB-18472, PDB-8qkv:
SWR1-nucleosome complex in configuration 2
Method: EM (single particle) / Resolution: 4.7 Å

Chemicals

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

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • Saccharomyces cerevisiae (brewer's yeast)
  • saccharomyces cerevisiae s288c (yeast)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN / Chromatin remodelling complex / nucleosome / protein-DNA complex

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