間白素結合因子 (Interleukin binding factor, ILF) 是一個轉錄因子可以和人類後天免疫不全病毒I型的長端點重複部份 (HIV-1 LTR) 的多嘌呤的序列以及間白素II型啟動子作結合。間白素結合因子的DNA結合區域 (the DNA-binding domain of ILF, ILF-DBD) 是屬於winged helix 蛋白質家族。這裡我們解出了一個解析度為2.4 Å含有兩個間白素結合因子的DNA結合區域與一條長度為16個鹼基對的DNA和鎂離子所形成複合體結構。在蛋白質的recognition helix (H3) 和 DNA 的major groove有許多直接和介由水為媒介的氫鍵形成。間白素結合因子在winged helix/forkhead 蛋白質家族中是屬於一個新的成員，因為它的C端□-helix的存在取代了的典型的wing 2結構並改變了C端鹼性胺基酸 (RKRRPR) 和DNA辨認的位向。此結構也展示出wing1和DNA的minor groove作用以及在helix 2和helix3之間的胺基酸 (Lys45) 會和DNA作用。比較ILF-DBD/DNA和HNF-3□/DNA這兩個複合體的結構呈現出此兩個蛋白質在DNA的TAAACA 核心區域以及DNA的兩端區域的DNA辨認有一些差異。綜合以上，這些結論提供了一些新的了解對於用高度相似的DNA結合區域在DNA binding的專一性上所做的調節，以及在高度相似的winged helix/forkhead 蛋白質家族中的蛋白質如何有不同的DNA結合特性。

Interleukin enhancer binding factor (ILF) is a transcription factor that binds to purine-rich regulatory motifs in both the human T-cell leukemia virus long terminal region (HILV-1 LTR) and the interleukin-2 (IL-2) promoter. The DNA-binding domain of ILF (ILF-DBD) belongs to a member of winged helix/forkhead family. Here we report a 2.4 Å crystal structure of two copies of the DBD of ILF bound to 16-bp DNA. Extensive contacts are formed between the recognition helix (H3) and the major groove of DNA through direct and water-mediated hydrogen bonds. ILF-DBD is a new member of the winged helix/forkhead proteins because the presence of a C-terminal α-helix (H4) in place of a typical wing 2 changes the orientation of the C-terminal basic residues (RKRRPR) of H4 to recognize DNA. The structure also shows that wing 1 interacts with minor groove of DNA, and the residues (Lys45) from the H2-H3 loop region make interactions with DNA. Comparison of the ILF-DBD/DNA complex with HNF-3□/DNA complex revealed some differences in DNA recognition at both the “TAAACA” core and the flanking regions of the DNA site. Taken together, these results offer new insights into the modulation of DNA binding specificity within a conserved DNA-binding domain, and provide how highly homologous winged helix/forkhead proteins exhibit differential DNA-binding properties.

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