2QQS

JMJD2A tandem tudor domains in complex with a trimethylated histone H4-K20 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor.

Lee, J.Thompson, J.R.Botuyan, M.V.Mer, G.

(2008) Nat Struct Mol Biol 15: 109-111

  • DOI: 10.1038/nsmb1326
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The lysine demethylase JMJD2A has the unique property of binding trimethylated peptides from two different histone sequences (H3K4me3 and H4K20me3) through its tudor domains. Here we show using X-ray crystallography and calorimetry that H3K4me3 and H ...

    The lysine demethylase JMJD2A has the unique property of binding trimethylated peptides from two different histone sequences (H3K4me3 and H4K20me3) through its tudor domains. Here we show using X-ray crystallography and calorimetry that H3K4me3 and H4K20me3, which are recognized with similar affinities by JMJD2A, adopt radically different binding modes, to the extent that we were able to design single point mutations in JMJD2A that inhibited the recognition of H3K4me3 but not H4K20me3 and vice versa.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
JmjC domain-containing histone demethylation protein 3AA, B118Homo sapiensMutation(s): 0 
Gene Names: JMJD2AJHDM3AJMJD2KIAA0677KDM4A
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
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
METHYLATED HISTONE H4 PEPTIDEC, D10N/AMutation(s): 0 
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
C,DL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.97α = 90
b = 27.689β = 90.77
c = 82.424γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance