5IKF

Crystal structure of the C-terminal domain of the Mit1 nucleosome remodeler in complex with Clr1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

SHREC Silences Heterochromatin via Distinct Remodeling and Deacetylation Modules.

Job, G.Brugger, C.Xu, T.Lowe, B.R.Pfister, Y.Qu, C.Shanker, S.Banos Sanz, J.I.Partridge, J.F.Schalch, T.

(2016) Mol Cell 62: 207-221

  • DOI: https://doi.org/10.1016/j.molcel.2016.03.016
  • Primary Citation of Related Structures:  
    5IKF, 5IKJ, 5IKK

  • PubMed Abstract: 

    Nucleosome remodeling and deacetylation (NuRD) complexes are co-transcriptional regulators implicated in differentiation, development, and diseases. Methyl-CpG binding domain (MBD) proteins play an essential role in recruitment of NuRD complexes to their target sites in chromatin. The related SHREC complex in fission yeast drives transcriptional gene silencing in heterochromatin through cooperation with HP1 proteins. How remodeler and histone deacetylase (HDAC) cooperate within NuRD complexes remains unresolved. We determined that in SHREC the two modules occupy distant sites on the scaffold protein Clr1 and that repressive activity of SHREC can be modulated by the expression level of the HDAC-associated Clr1 domain alone. Moreover, the crystal structure of Clr2 reveals an MBD-like domain mediating recruitment of the HDAC module to heterochromatin. Thus, SHREC bi-functionality is organized in two separate modules with separate recruitment mechanisms, which work together to elicit transcriptional silencing at heterochromatic loci.


  • Organizational Affiliation

    Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin remodeling factor mit1262Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: mit1SPBP35G2.10
EC: 3.6.4
UniProt
Find proteins for Q9P793 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9P793 
Go to UniProtKB:  Q9P793
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P793
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cryptic loci regulator protein 1155Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: clr1SPBC2D10.17
UniProt
Find proteins for O74808 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O74808 
Go to UniProtKB:  O74808
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74808
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.68α = 90
b = 52.85β = 115.63
c = 81.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandPP00P3_139137-1

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references