6RR0

Crystal structure of the Sir4 H-BRCT domain in complex with Ubp10 pT123 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Sir4 H-BRCT domain interacts with phospho-proteins to sequester and repress yeast heterochromatin.

Deshpande, I.Keusch, J.J.Challa, K.Iesmantavicius, V.Gasser, S.M.Gut, H.

(2019) EMBO J 38: e101744-e101744

  • DOI: https://doi.org/10.15252/embj.2019101744
  • Primary Citation of Related Structures:  
    6QSZ, 6QTM, 6RR0, 6RRV

  • PubMed Abstract: 

    In Saccharomyces cerevisiae, the silent information regulator (SIR) proteins Sir2/3/4 form a complex that suppresses transcription in subtelomeric regions and at the homothallic mating-type (HM) loci. Here, we identify a non-canonical BRCA1 C-terminal domain (H-BRCT) in Sir4, which is responsible for tethering telomeres to the nuclear periphery. We show that Sir4 H-BRCT and the closely related Dbf4 H-BRCT serve as selective phospho-epitope recognition domains that bind to a variety of phosphorylated target peptides. We present detailed structural information about the binding mode of established Sir4 interactors (Esc1, Ty5, Ubp10) and identify several novel interactors of Sir4 H-BRCT, including the E3 ubiquitin ligase Tom1. Based on these findings, we propose a phospho-peptide consensus motif for interaction with Sir4 H-BRCT and Dbf4 H-BRCT. Ablation of the Sir4 H-BRCT phospho-peptide interaction disrupts SIR-mediated repression and perinuclear localization. In conclusion, the Sir4 H-BRCT domain serves as a hub for recruitment of phosphorylated target proteins to heterochromatin to properly regulate silencing and nuclear order.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory protein SIR4
A, B, C, D, E
A, B, C, D, E, F, G
127Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SIR4ASD1STE9UTH2YDR227WYD9934.12
UniProt
Find proteins for P11978 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P11978 
Go to UniProtKB:  P11978
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11978
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 10
H, I, J, K, L
H, I, J, K, L, M, N
12Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.19.12
UniProt
Find proteins for P53874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53874 
Go to UniProtKB:  P53874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53874
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
H, I, J, K, L
H, I, J, K, L, M, N
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.04α = 90
b = 75.28β = 97.24
c = 95.91γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references