Structure of KIAA1718 Jumonji domain

Experimental Data Snapshot

  • Resolution: 2.29 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 

Starting Model: experimental
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Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.

Horton, J.R.Upadhyay, A.K.Qi, H.H.Zhang, X.Shi, Y.Cheng, X.

(2010) Nat Struct Mol Biol 17: 38-43

  • DOI: https://doi.org/10.1038/nsmb.1753
  • Primary Citation of Related Structures:  
    3KV4, 3KV5, 3KV6, 3KV9, 3KVA, 3KVB

  • PubMed Abstract: 

    Combinatorial readout of multiple covalent histone modifications is poorly understood. We provide insights into how an activating histone mark, in combination with linked repressive marks, is differentially 'read' by two related human demethylases, PHF8 and KIAA1718 (also known as JHDM1D). Both enzymes harbor a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2. The presence of H3K4me3 on the same peptide as H3K9me2 makes the doubly methylated peptide a markedly better substrate of PHF8, whereas the presence of H3K4me3 has the opposite effect, diminishing the H3K9me2 demethylase activity of KIAA1718 without adversely affecting its H3K27me2 activity. The difference in substrate specificity between the two is explained by PHF8 adopting a bent conformation, allowing each of its domains to engage its respective target, whereas KIAA1718 adopts an extended conformation, which prevents its access to H3K9me2 by its jumonji domain when its PHD engages H3K4me3.

  • Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
JmjC domain-containing histone demethylation protein 1D397Homo sapiensMutation(s): 0 
Gene Names: JHDM1DKIAA1718
EC: 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZMT4 (Homo sapiens)
Explore Q6ZMT4 
Go to UniProtKB:  Q6ZMT4
GTEx:  ENSG00000006459 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZMT4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.29 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.9α = 90
b = 77.9β = 90
c = 289.7γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description