2C6Y

Crystal structure of interleukin enhancer-binding factor 1 bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Human Foxk1A-DNA Complex and its Implications on the Diverse Binding Specificity of Winged Helix/Forkhead Proteins.

Tsai, K.-L.Huang, C.-Y.Chang, C.-H.Sun, Y.-J.Chuang, W.-J.Hsiao, C.-D.

(2006) J.Biol.Chem. 281: 17400

  • DOI: 10.1074/jbc.M600478200

  • PubMed Abstract: 
  • Interleukin enhancer binding factor (ILF) is a human transcription factor and a new member of the winged helix/forkhead family. ILF can bind to purine-rich regulatory motifs such as the human T-cell leukemia virus-long terminal region and the interle ...

    Interleukin enhancer binding factor (ILF) is a human transcription factor and a new member of the winged helix/forkhead family. ILF can bind to purine-rich regulatory motifs such as the human T-cell leukemia virus-long terminal region and the interleukin-2 promoter. Here we report the 2.4 A crystal structure of two DNA binding domains of ILF (FOXK1a) binding to a 16-bp DNA duplex containing a promoter sequence. Electrophoretic mobility shift assay studies demonstrate that two ILF-DNA binding domain molecules cooperatively bind to DNA. In addition to the recognition helix recognizing the core sequences through the major groove, the structure shows that wing 1 interacts with the minor groove of DNA, and the H2-H3 loop region makes ionic bonds to the phosphate group, which permits the recognition of DNA. The structure also reveals that the presence of the C-terminal alpha-helix in place of a typical wing 2 in a member of this family alters the orientation of the C-terminal basic residues (RKRRPR) when binding to DNA outside the core sequence. These results provide a new insight into how the DNA binding specificities of winged helix/forkhead proteins may be regulated by their less conserved regions.


    Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FORKHEAD BOX PROTEIN K2
A, B
111Homo sapiensMutation(s): 0 
Gene Names: FOXK2 (ILF, ILF1)
Find proteins for Q01167 (Homo sapiens)
Go to Gene View: FOXK2
Go to UniProtKB:  Q01167
Entity ID: 2
MoleculeChainsLengthOrganism
INTERLEUKIN 2 PROMOTORC16Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
INTERLEUKIN 2 PROMOTORD16Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.233 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.736α = 90.00
b = 58.736β = 90.00
c = 324.923γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
CNSrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance