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Integrative Modeling of a Sin3/HDAC Complex Sub-structure.

Charles A S Banks1, Ying Zhang1, Sayem Miah1

  • 1Stowers Institute for Medical Research, Kansas City, MO 64110, USA.

Cell Reports
|April 16, 2020
PubMed
Summary
This summary is machine-generated.

Researchers mapped the Sin3 complex structure using crosslinking mass spectrometry. This revealed the spatial arrangement of Sin3 subunits around the SIN3A scaffold, clarifying how they influence HDAC1 activity.

Keywords:
DSSOHDACSin3XL-MSchromatincrosslinkingdistance restraintsprotein dockingproteomicsstructural modeling

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Area of Science:

  • Molecular Biology
  • Chromatin Biology
  • Structural Biology

Background:

  • Sin3/HDAC complexes regulate gene expression through histone deacetylation and chromatin condensation.
  • The assembly and structural organization of Sin3/HDAC subunits around the SIN3A scaffold remain incompletely understood.

Purpose of the Study:

  • To characterize the spatial arrangement of Sin3 subunits within the Sin3 complex.
  • To elucidate the structural organization of subunits around the SIN3A scaffolding protein.

Main Methods:

  • Employed Halo affinity capture, chemical crosslinking, and high-resolution mass spectrometry (XL-MS).
  • Determined intersubunit distance constraints by identifying interprotein and self-crosslinks for 13 Sin3 subunits.
  • Utilized crosslinking data to guide the assembly of a Sin3 complex substructure.

Main Results:

  • Identified 66 interprotein and 63 self-crosslinks, validating the approach with existing structural data.
  • Determined the relative positions of SAP30L, HDAC1, SUDS3, HDAC2, and ING1 subunits around the SIN3A scaffold.
  • Revealed the architecture of a Sin3 complex subassembly, indicating space for additional factors.

Conclusions:

  • The study provides a structural map of a Sin3 complex substructure, detailing subunit organization.
  • The findings suggest a flexible architecture allowing multiple factors to modulate the activity of the catalytic subunit HDAC1.