Crystal structure of the first Tudor domain of human PHF20

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53.

Cui, G.Park, S.Badeaux, A.I.Kim, D.Lee, J.Thompson, J.R.Yan, F.Kaneko, S.Yuan, Z.Botuyan, M.V.Bedford, M.T.Cheng, J.Q.Mer, G.

(2012) Nat Struct Mol Biol 19: 916-924

  • DOI: https://doi.org/10.1038/nsmb.2353
  • Primary Citation of Related Structures:  
    2LDM, 3P8D, 3SD4

  • PubMed Abstract: 

    PHF20 is a multidomain protein and subunit of a lysine acetyltransferase complex that acetylates histone H4 and p53 but whose function is unclear. Using biochemical, biophysical and cellular approaches, we determined that PHF20 is a direct regulator of p53. A Tudor domain in PHF20 recognized p53 dimethylated at Lys370 or Lys382 and a homodimeric form of this Tudor domain could associate with the two dimethylated sites on p53 with enhanced affinity, indicating a multivalent interaction. Association with PHF20 promotes stabilization and activation of p53 by diminishing Mdm2-mediated p53 ubiquitylation and degradation. PHF20 contributes to upregulation of p53 in response to DNA damage, and ectopic expression of PHF20 in different cell lines leads to phenotypic changes that are hallmarks of p53 activation. Overall our work establishes that PHF20 functions as an effector of p53 methylation that stabilizes and activates p53.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger protein 20
A, B
69Homo sapiensMutation(s): 0 
Gene Names: PHF20C20orf104GLEA2HCA58NZFTZP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVI0 (Homo sapiens)
Explore Q9BVI0 
Go to UniProtKB:  Q9BVI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BVI0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.746α = 90
b = 60.761β = 112.82
c = 37.75γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
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: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-08-15
    Changes: Database references
  • Version 1.3: 2012-09-26
    Changes: Database references
  • Version 1.4: 2019-11-06
    Changes: Data collection, Database references