4HCZ

PHF1 Tudor in complex with H3K36me3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1.

Musselman, C.A.Avvakumov, N.Watanabe, R.Abraham, C.G.Lalonde, M.E.Hong, Z.Allen, C.Roy, S.Nunez, J.K.Nickoloff, J.Kulesza, C.A.Yasui, A.Cote, J.Kutateladze, T.G.

(2012) Nat.Struct.Mol.Biol. 19: 1266-1272

  • DOI: 10.1038/nsmb.2435

  • PubMed Abstract: 
  • The PHD finger protein 1 (PHF1) is essential in epigenetic regulation and genome maintenance. Here we show that the Tudor domain of human PHF1 binds to histone H3 trimethylated at Lys36 (H3K36me3). We report a 1.9-Å resolution crystal structure of th ...

    The PHD finger protein 1 (PHF1) is essential in epigenetic regulation and genome maintenance. Here we show that the Tudor domain of human PHF1 binds to histone H3 trimethylated at Lys36 (H3K36me3). We report a 1.9-Å resolution crystal structure of the Tudor domain in complex with H3K36me3 and describe the molecular mechanism of H3K36me3 recognition using NMR. Binding of PHF1 to H3K36me3 inhibits the ability of the Polycomb PRC2 complex to methylate Lys27 of histone H3 in vitro and in vivo. Laser microirradiation data show that PHF1 is transiently recruited to DNA double-strand breaks, and PHF1 mutants impaired in the H3K36me3 interaction exhibit reduced retention at double-strand break sites. Together, our findings suggest that PHF1 can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response.


    Organizational Affiliation

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHD finger protein 1
A, B
58Homo sapiensMutation(s): 0 
Gene Names: PHF1 (PCL1)
Find proteins for O43189 (Homo sapiens)
Go to Gene View: PHF1
Go to UniProtKB:  O43189
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H3L-like histone
C, D
10Homo sapiensMutation(s): 0 
Find proteins for Q6TXQ4 (Homo sapiens)
Go to UniProtKB:  Q6TXQ4
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
C, D
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.030α = 90.00
b = 29.670β = 116.41
c = 62.000γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
CrystalCleardata collection
PHENIXrefinement
PHASERphasing
d*TREKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2012-12-19
    Type: Database references