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 

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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 interleukin-2 promoter ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FORKHEAD BOX PROTEIN K2A, B111Homo sapiensMutation(s): 0 
Gene Names: FOXK2, ILF, ILF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q01167 (Homo sapiens)
Explore Q01167 
Go to UniProtKB:  Q01167
PHAROS:  Q01167
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01167
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
INTERLEUKIN 2 PROMOTORC 16Homo sapiens
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
INTERLEUKIN 2 PROMOTORD 16Homo sapiens
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth A],
F [auth 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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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