2C6Y

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.233 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    2C6Y

  • 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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FORKHEAD BOX PROTEIN K2A, B111Homo sapiensMutation(s): 0 
Gene Names: FOXK2, ILF, ILF1
Find proteins for Q01167 (Homo sapiens)
Explore Q01167 
Go to UniProtKB:  Q01167
NIH Common Fund Data Resources
PHAROS  Q01167
GTEx  ENSG00000141568
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    INTERLEUKIN 2 PROMOTORC16Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      INTERLEUKIN 2 PROMOTORD16Homo sapiens
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MG
      Query on MG
      Download CCD File 
      A, B
      		MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.40 Å
      • R-Value Free: 0.258 
      • R-Value Work: 0.233 
      • R-Value Observed: 0.233 
      • Space Group: P 61 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 58.736α = 90
      b = 58.736β = 90
      c = 324.923γ = 120
      Software Package:
      Software NamePurpose
      CNSrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      SOLVEphasing

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History 

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