9M74 | pdb_00009m74

Crystal structure of MBP-fused BIL1/BZR1 (21-104) in complex with double-stranded DNA contaning CACAGCTGTG

• PDB DOI: https://doi.org/10.2210/pdb9M74/pdb
• NAKB: 9M74

• Classification: DNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana, synthetic construct
• Expression System: Escherichia coli BL21(DE3), synthetic construct
• Mutation(s): Yes 


• Deposited: 2025-03-09 Released: 2025-09-10 
• Deposition Author(s): Shohei, N., Masaru, T., Takuya, M.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 
  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Single cis-elements in brassinosteroid-induced upregulated genes are insufficient to recruit both redox states of the BIL1/BZR1 DNA-binding domain.

Nosaki, S., Ohtsuka, M., Nakano, T., Tanokura, M., Miyakawa, T.

(2025) FEBS Lett 599: 3369-3380

• PubMed: 40882013 
• DOI: https://doi.org/10.1002/1873-3468.70147
• Primary Citation of Related Structures:  
  9M73, 9M74


• PubMed Abstract: 
  

  The plant-specific transcription factor BRZ-INSENSITIVE-LONG 1 (BIL1)/BRASSINAZOLE-RESISTANT 1 (BZR1) regulates the growth of Arabidopsis thaliana via brassinosteroid signaling, acting as both a gene repressor and activator. Its upregulation requires environmental cues mediated by PHYTOCHROME INTERACTING FACTOR 4 (PIF4), with oxidative modifications via H ₂ O ₂ enhancing their interaction. However, the nature of the tripartite complex of cis-elements, BIL1/BZR1, and PIF4 under redox changes remains unclear. Here, we demonstrate that oxidation of the DNA-binding domain (DBD) of BIL1/BZR1 alters its DNA-binding ability. However, single cis-elements enriched in brassinosteroid-induced genes do not support binding of either redox form, nor does BIL1/BZR1 DBD heterodimerize with PIF4 DBD on these elements. These findings highlight the complexity of brassinosteroid transcriptional regulation beyond DNA-binding specificity and redox modifications.

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Organizational Affiliation: 
• Institute of Life and Environmental Sciences, University of Tsukuba, Japan.
Tsukuba Plant-Innovation Research Center (T-PIRC), University of Tsukuba, Japan.
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.
Graduate School of Biostudies, Kyoto University, Japan.

Biological Assembly 1  

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

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

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 219.21 kDa 
• Atom Count: 15,101 
• Modeled Residue Count: 1,806 
• Deposited Residue Count: 1,872 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1	A [auth C], B [auth D], E [auth A], F [auth B]	453	Arabidopsis thaliana	Mutation(s): 8  Gene Names: malE, JW3994, BZR1, BIS2, At1g75080, F9E10.7
UniProt
Find proteins for Q8S307 (Arabidopsis thaliana) Explore Q8S307  Go to UniProtKB:  Q8S307

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*CP*AP*CP*AP*GP*CP*TP*GP*TP*GP*AP*AP*A)-3')	C [auth G], D [auth H], G [auth E], H [auth F]	15	synthetic construct

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	I [auth J], J [auth K], K [auth L], L [auth M]	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	M [auth C], N [auth A], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	I [auth J], J [auth K], K [auth L], L [auth M]	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free:  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.84	α = 90
b = 92.506	β = 100.167
c = 111.736	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Shohei, N., Masaru, T., Takuya, M.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H04855
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H04855
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP19K23658
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21H02114
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101077
Japan Agency for Medical Research and Development (AMED)	Japan	JP24ama121010

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Database references