9M73 | pdb_00009m73

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

PDB DOI: https://doi.org/10.2210/pdb9M73/pdb
NAKB: 9M73

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.245 (Depositor), 0.247 (DCC)
R-Value Work:
0.205 (Depositor), 0.207 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
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 ₂O 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.

Organizational Affiliation

Institute of Life and Environmental Sciences, University of Tsukuba, Japan.

Macromolecule Content

Total Structure Weight: 219.33 kDa
Atom Count: 15,075
Modeled Residue Count: 1,805
Deposited Residue Count: 1,872
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8S307
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
E-box(CATATG)-containing DNA	C [auth G], D [auth H], G [auth E], H [auth F]	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

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	Interactions Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M] Interactions & Density Focus chain I [auth J] Focus chain J [auth K] Focus chain K [auth L] Focus chain L [auth M]
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	M [auth C], N [auth A], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain M [auth C] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.245 (Depositor), 0.247 (DCC)
R-Value Work: 0.205 (Depositor), 0.207 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.848	α = 90
b = 92.602	β = 100.323
c = 111.767	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Shohei, N.

Masaru, T.

Takuya, M.

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP17H05835
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP19H04855
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP19K23658
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP21H02114
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101077
Japan Agency for Medical Research and Development (AMED)	Japan	JP24ama121010