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: 2.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 

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: 10.1016/j.molcel.2016.03.016
  • Primary Citation of Related Structures:  

  • 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 t ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chromatin remodeling factor mit1
A
262Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: mit1
EC: 3.6.4.-
Find proteins for Q9P793 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9P793
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cryptic loci regulator protein 1
B
155Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: clr1
Find proteins for O74808 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74808
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.680α = 90.00
b = 52.850β = 115.63
c = 81.970γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandPP00P3_139137-1

Revision History 

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