8XUF

CDF1 Dof domain in palindromic-bound complex with DNA duplex

Summary for 8XUF

• Entry DOI: 10.2210/pdb8xuf/pdb
• Descriptor: DNA (5'-D(*TP*TP*CP*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*CP*TP*TP*TP*AP*TP*G)-3'), DNA (5'-D(*AP*AP*CP*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*CP*TP*TP*TP*AP*TP*G)-3'), CDF1, ... (5 entities in total)
• Functional Keywords: plant-specific transcription factor, gene supression, cis-element, zinc finger, dna binding protein, dna-dna binding protein complex, dna/dna binding protein
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 4
• Total formula weight: 27243.95

Authors

Furihata, H.,Tanokura, M.,Miyakawa, T. (deposition date: 2024-01-12, release date: 2025-03-12, Last modification date: 2025-05-07)

Primary citation

Furihata, H.,Zhu, Z.,Nishida, K.,Sakuraba, Y.,Tsuji, A.,Yamashita, H.,Nosaki, S.,Tachibana, R.,Yamagami, A.,Ikeda, Y.,Abe, M.,Sawasaki, T.,Nakano, T.,Yanagisawa, S.,Tanokura, M.,Miyakawa, T.
Structural insights into CDF1 accumulation on the CONSTANS promoter via a plant-specific DNA-binding domain.
Nat.Plants, 11:836-848, 2025

PubMed Abstract: DNA-binding with one-finger (Dof) proteins are a family of plant-specific transcription factors distinguished by the highly conserved Dof DNA-binding domain. Various members play crucial roles in diverse plant biological processes. However, it remains unclear how the Dof domain recognizes a restricted set of promoters for gene regulation by binding to just four nucleotides, AAAG/CTTT. Here we present the crystal structure of the Dof domain of CYCLING DOF FACTOR 1 (CDF1), a well-characterized Dof protein acting as a transcriptional repressor by binding to the CONSTANS promoter to regulate photoperiodic flowering, in complex with DNA containing two cis elements. The data reveal that the Dof domain exhibits a unique zinc ribbon fold that includes a three-stranded antiparallel β-sheet and a carboxy-terminal loop, enabling DNA recognition accompanied by directional expansion of the major groove. These features facilitate binding to contiguous target cis elements in a proper arrangement to effectively regulate gene expression.

PubMed: 40263610
DOI: 10.1038/s41477-025-01946-6

Experimental method

X-RAY DIFFRACTION (2.3 Å)