5IKK | pdb_00005ikk

Structure of the histone deacetylase Clr3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5IKK

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 74.52 kDa 
  • Atom Count: 4,952 
  • Modeled Residue Count: 594 
  • Deposited Residue Count: 657 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone deacetylase clr3657Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: clr3SPBC800.03
EC: 3.5.1.98
UniProt
Find proteins for P56523 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P56523 
Go to UniProtKB:  P56523
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56523
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
L [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A],
D [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3

Query on NO3



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
C [auth A],
E [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
M [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.487α = 90
b = 187.259β = 90
c = 142.633γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description