5D6Y

Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 

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 microar ...

    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 4AABCDEF121Homo sapiensMutation(s): 0 
Gene Names: KDM4AJHDM3AJMJD2JMJD2AKIAA0677
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
Find proteins for O75164 (Homo sapiens)
Explore O75164 
Go to UniProtKB:  O75164
NIH Common Fund Data Resources
PHAROS  O75164
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
peptide H3K23me3 (19-28)abcd10Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
a,b,c,dL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 
  • Space Group: P 32
  • Diffraction Data DOI: 10.18430/m35d6y Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.159α = 90
b = 106.159β = 90
c = 79.206γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

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 StatesU01GM098248
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R37GM059785-15/P250VA

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-12-07
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence