3ZCO

Crystal structure of S. cerevisiae Sir3 C-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Dimerization of Sir3 Via its C-Terminal Winged Helix Domain is Essential for Yeast Heterochromatin Formation.

Oppikofer, M.Kueng, S.Keusch, J.J.Hassler, M.Ladurner, A.G.Gut, H.Gasser, S.M.

(2013) EMBO J 32: 437

  • DOI: https://doi.org/10.1038/emboj.2012.343
  • Primary Citation of Related Structures:  
    3ZCO

  • PubMed Abstract: 

    Gene silencing in budding yeast relies on the binding of the Silent Information Regulator (Sir) complex to chromatin, which is mediated by extensive interactions between the Sir proteins and nucleosomes. Sir3, a divergent member of the AAA+ ATPase-like family, contacts both the histone H4 tail and the nucleosome core. Here, we present the structure and function of the conserved C-terminal domain of Sir3, comprising 138 amino acids. This module adopts a variant winged helix-turn-helix (wH) architecture that exists as a stable homodimer in solution. Mutagenesis shows that the self-association mediated by this domain is essential for holo-Sir3 dimerization. Its loss impairs Sir3 loading onto nucleosomes in vitro and eliminates silencing at telomeres and HM loci in vivo. Replacing the Sir3 wH domain with an unrelated bacterial dimerization motif restores both HM and telomeric repression in sir3Δ cells. In contrast, related wH domains of archaeal and human members of the Orc1/Sir3 family are monomeric and have DNA binding activity. We speculate that a dimerization function for the wH evolved with Sir3's ability to facilitate heterochromatin formation.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Basel 4058, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
REGULATORY PROTEIN SIR3141Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P06701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06701 
Go to UniProtKB:  P06701
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06701
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.218 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.32α = 90
b = 75.32β = 90
c = 55.57γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references, Other