3IUF

Crystal structure of the C2H2-type zinc finger domain of human ubi-d4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the Cys2His2-type zinc finger domain of human DPF2.

Zhang, W.Xu, C.Bian, C.Tempel, W.Crombet, L.MacKenzie, F.Min, J.Liu, Z.Qi, C.

(2011) Biochem Biophys Res Commun 413: 58-61

  • DOI: 10.1016/j.bbrc.2011.08.043
  • Primary Citation of Related Structures:  
    3IUF

  • PubMed Abstract: 
  • DPF2 is an evolutionary highly conserved member of the d4-protein family characterized by an N-terminal 2/3 domain, a C2H2-type zinc finger (ZF), and a C-terminal tandem PHD zinc finger. DPF2 is identified as a transcription factor and may be related ...

    DPF2 is an evolutionary highly conserved member of the d4-protein family characterized by an N-terminal 2/3 domain, a C2H2-type zinc finger (ZF), and a C-terminal tandem PHD zinc finger. DPF2 is identified as a transcription factor and may be related with some cancers in human. Here, we report the crystal structure of the C2H2-type zinc finger domain of human DPF2 with a canonical C2H2 fold, which contains two beta strands and one alpha helix. Several conserved residues, including Lys207, Lys216 and Arg217, constitute a positively charged surface in C2H2 domain, which implicates that it has the potential to bind DNA. The side chains of the residues Y209, C211, C214, K216, Y218, L224, H227 and H232 form the hydrophobic core of C2H2 domain, which indicates a potential-binding surface in the human DPF2.


    Organizational Affiliation

    Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger protein ubi-d4A48Homo sapiensMutation(s): 0 
Gene Names: DPF2REQUBID4BAF45D
Find proteins for Q92785 (Homo sapiens)
Explore Q92785 
Go to UniProtKB:  Q92785
NIH Common Fund Data Resources
PHAROS  Q92785
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.714α = 90
b = 57.657β = 90
c = 22.585γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-02
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description