4UC4

Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Reader domain specificity and lysine demethylase-4 family function.

Su, Z.Wang, F.Lee, J.H.Stephens, K.E.Papazyan, R.Voronina, E.Krautkramer, K.A.Raman, A.Thorpe, J.J.Boersma, M.D.Kuznetsov, V.I.Miller, M.D.Taverna, S.D.Phillips, G.N.Denu, J.M.

(2016) Nat Commun 7: 13387-13387

  • DOI: 10.1038/ncomms13387
  • Primary Citation of Related Structures:  
    4UC4, 5D6X, 5D6W, 5D6Y

  • PubMed Abstract: 
  • The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microarray ...

    The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microarray analysis uncovers trimethyl-lysine histone-binding preferences among the closely related KDM4 double tudor domains (DTDs). KDM4A/B DTDs bind strongly to H3K23me3, a poorly understood histone modification recently shown to be enriched in meiotic chromatin of ciliates and nematodes. The 2.28 Å co-crystal structure of KDM4A-DTD in complex with H3K23me3 peptide reveals key intermolecular interactions for H3K23me3 recognition. Furthermore, analysis of the 2.56 Å KDM4B-DTD crystal structure pinpoints the underlying residues required for exclusive H3K23me3 specificity, an interaction supported by in vivo co-localization of KDM4B and H3K23me3 at heterochromatin in mammalian meiotic and newly postmeiotic spermatocytes. In vitro demethylation assays suggest H3K23me3 binding by KDM4B stimulates H3K36 demethylation. Together, these results provide a possible mechanism whereby H3K23me3-binding by KDM4B directs localized H3K36 demethylation during meiosis and spermatogenesis.


    Organizational Affiliation

    Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 4B AB119Homo sapiensMutation(s): 0 
Gene Names: KDM4BJHDM3BJMJD2BKIAA0876
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt)
Find proteins for O94953 (Homo sapiens)
Explore O94953 
Go to UniProtKB:  O94953
NIH Common Fund Data Resources
PHAROS:  O94953
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.203 
  • Space Group: P 31
  • Diffraction Data DOI: 10.18430/m34uc4 Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.436α = 90
b = 77.436β = 90
c = 50.758γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM098248
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM059785-15/P250VA

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references, Derived calculations
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence