Crystal structure of tudor domain 2 of human PHD finger protein 20

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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This is version 1.5 of the entry. See complete history


Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins.

Adams-Cioaba, M.A.Li, Z.Tempel, W.Guo, Y.Bian, C.Li, Y.Lam, R.Min, J.

(2012) FEBS Lett 586: 859-865

  • DOI: https://doi.org/10.1016/j.febslet.2012.02.012
  • Primary Citation of Related Structures:  
    3Q1J, 3QII

  • PubMed Abstract: 

    The human PHD finger protein 20 (PHF20) is a putative transcription factor. While little is known about its cognate cellular role, antibodies against PHF20 are present in sera from patients with hepatocellular carcinoma, glioblastoma and childhood medulloblastula. PHF20 comprises two N-terminal Tudor domains, a central C2H2-link zinc finger domain and a C-terminal zinc-binding PHD domain, and is a component of some MLL methyltransferase complexes. Here, we report the crystal structures of the N-terminal Tudor domains of PHF20 and highlight the novel structural features of each domain. We also confirm previous studies suggesting that the second Tudor domain of PHF20 exhibits preference for dimethylated histone substrates.

  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger protein 2085Homo sapiensMutation(s): 0 
Gene Names: PHF20C20orf104GLEA2HCA58NZFTZP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVI0 (Homo sapiens)
Explore Q9BVI0 
Go to UniProtKB:  Q9BVI0
GTEx:  ENSG00000025293 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BVI0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on UNX

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.683α = 90
b = 48.683β = 90
c = 96.273γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-07
    Changes: Database references
  • Version 1.3: 2012-04-11
    Changes: Database references
  • Version 1.4: 2017-11-08
    Changes: Refinement description
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Refinement description