8XUF | pdb_00008xuf

CDF1 Dof domain in palindromic-bound complex with DNA duplex

• PDB DOI: https://doi.org/10.2210/pdb8XUF/pdb
• NAKB: 8XUF

• Classification: DNA/DNA BINDING PROTEIN
• Organism(s): synthetic construct, Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-12 Released: 2025-03-12 
• Deposition Author(s): Furihata, H., Tanokura, M., Miyakawa, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: in silico

Literature

Structural insights into CDF1 accumulation on the CONSTANS promoter via a plant-specific DNA-binding domain.

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.

(2025) Nat Plants 11: 836-848

• PubMed: 40263610 
• DOI: https://doi.org/10.1038/s41477-025-01946-6
• Primary Citation of Related Structures:  
  8XUF


• 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.

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Organizational Affiliation: 
• Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
Proteo-Science Center, Ehime University, Matsuyama, Japan.
Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
Graduate School of Engineering Science, The University of Osaka, Osaka, Japan.
Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.
Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. [e-mail].
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. [e-mail].
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. [e-mail].
Graduate School of Biostudies, Kyoto University, Kyoto, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 27.24 kDa 
• Atom Count: 1,656 
• Modeled Residue Count: 142 
• Deposited Residue Count: 170 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CDF1	C, D	65	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CDF1, DOF5.5, At5g62430, K19B1.4, MMI9.24
UniProt
Find proteins for Q8W1E3 (Arabidopsis thaliana) Explore Q8W1E3  Go to UniProtKB:  Q8W1E3

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*CP*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*CP*TP*TP*TP*AP*TP*G)-3')	A	20	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*CP*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*CP*TP*TP*TP*AP*TP*G)-3')	B	20	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth C], F [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.442	α = 90
b = 79.442	β = 90
c = 93.729	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Furihata, H., Tanokura, M., Miyakawa, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22H04977
Japan Society for the Promotion of Science (JSPS)	Japan	19H04855
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121001
Japan Agency for Medical Research and Development (AMED)	Japan	24ama121010j0003

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-05-07
  Changes: Database references