3KQI

crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation.

Wen, H.Li, J.Song, T.Lu, M.Kan, P.Y.Lee, M.G.Sha, B.Shi, X.

(2010) J Biol Chem 285: 9322-9326

  • DOI: https://doi.org/10.1074/jbc.C109.097667
  • Primary Citation of Related Structures:  
    3KQI

  • PubMed Abstract: 

    Distinct lysine methylation marks on histones create dynamic signatures deciphered by the "effector" modules, although the underlying mechanisms remain unclear. We identified the plant homeodomain- and Jumonji C domain-containing protein PHF2 as a novel histone H3K9 demethylase. We show in biochemical and crystallographic analyses that PHF2 recognizes histone H3K4 trimethylation through its plant homeodomain finger and that this interaction is essential for PHF2 occupancy and H3K9 demethylation at rDNA promoters. Our study provides molecular insights into the mechanism by which distinct effector domains within a protein cooperatively modulate the "cross-talk" of histone modifications.


  • Organizational Affiliation

    Centers for Cancer Epigenetics, Houston, Texas 77030; Molecular and Cellular Oncology, Houston, Texas 77030.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger protein 275Homo sapiensMutation(s): 0 
Gene Names: KIAA0662PHF2
UniProt & NIH Common Fund Data Resources
Find proteins for O75151 (Homo sapiens)
Explore O75151 
Go to UniProtKB:  O75151
PHAROS:  O75151
GTEx:  ENSG00000197724 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75151
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H3K4Me3 peptide12Homo sapiensMutation(s): 0 
Gene Names: H3C1H3C2H3C3H3C4H3C6H3C7H3C8H3C10H3C11H3C12
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68431
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.757α = 90
b = 77.758β = 90
c = 72.116γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-02-13
    Changes: Advisory, Data collection, Derived calculations