Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.75 kDa 
• Atom Count: 1782 
• Residue Count: 218 
• Unique protein chains: 1

4UC4

Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B

• DOI: 10.2210/pdb4UC4/pdb

• Classification: REPLICATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-13 Released: 2016-03-16 
• Deposition Author(s): Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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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 

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

• PubMed: 27841353 
• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4B	A, B	119	Homo sapiens	Mutation(s): 0  Gene Names: KDM4B, JHDM3B, JMJD2B, KIAA0876 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 GTEx:  ENSG00000127663

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 = 77.436	α = 90
b = 77.436	β = 90
c = 50.758	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-08-13 
• Released Date: 2016-03-16 
Deposition Author(s): Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM098248
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM059785-15/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