3QII

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger protein 20A85Homo sapiensMutation(s): 0 
Gene Names: PHF20C20orf104GLEA2HCA58NZFTZP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVI0 (Homo sapiens)
Explore Q9BVI0 
Go to UniProtKB:  Q9BVI0
PHAROS:  Q9BVI0
GTEx:  ENSG00000025293 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BVI0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download Ideal Coordinates CCD File 
B [auth A]UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
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: 2011-02-09
    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