Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 35466.10 
• Atom Count: 2259 
• Residue Count: 254 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2C6Y

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

• DOI: 10.2210/pdb2C6Y/pdb
• NDB: PD0932

• Classification: TRANSCRIPTION REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2005-11-15 Released: 2006-04-18 
• Deposition Author(s): Tsai, K.-L., Huang, C.-Y., Chang, C.-H., Sun, Y.-J., Chuang, W.-J., Hsiao, C.-D.

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Experimental Data Snapshot

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

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

• PubMed: 16624804 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
FORKHEAD BOX PROTEIN K2	A, B	111	Homo sapiens	Mutation(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
Molecule	Chains	Length	Organism
INTERLEUKIN 2 PROMOTOR	C	16	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism
INTERLEUKIN 2 PROMOTOR	D	16	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 58.736	α = 90.00
b = 58.736	β = 90.00
c = 324.923	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
HKL-2000	data reduction
CNS	refinement
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-11-15 
• Released Date: 2006-04-18 
• Deposition Author(s): Tsai, K.-L., Huang, C.-Y., Chang, C.-H., Sun, Y.-J., Chuang, W.-J., Hsiao, C.-D.

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