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We determined the cryo-EM structure of the SIN3-HDAC Rpd3L complex, revealing an asymmetric architecture with two distinct arms. This structure explains how the complex organizes and targets histone deacetylase to chromatin.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Epigenetics

Background:

  • SIN3-HDAC complexes regulate gene expression via histone deacetylation.
  • Understanding their structure is crucial for elucidating chromatin regulation mechanisms.

Purpose of the Study:

  • To determine the cryo-electron microscopy (cryo-EM) structure of the budding yeast SIN3-HDAC complex Rpd3L.
  • To elucidate the organizational mechanism and histone deacetylase targeting strategy of the complex.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) at 2.6 Å resolution.
  • Structural analysis of the SIN3-HDAC Rpd3L complex.

Main Results:

  • The Rpd3L complex exhibits an asymmetric architecture with a T-shaped scaffold and two distinct arms (ARM1 and ARM2).
  • ARM1 sequesters the histone deacetylase Rpd3 in an inhibited state, while ARM2 exposes Rpd3's active site.
  • This structure differs from other class I HDAC complexes, highlighting a unique organization.

Conclusions:

  • The study reveals the structural basis for SIN3-HDAC complex organization.
  • Provides insights into how the complex targets histone deacetylase (HDAC) activity to chromatin.
  • The asymmetric structure suggests distinct functional roles for the two arms in regulating Rpd3 activity.