PDB-9m73: Crystal structure of MBP-fused BIL1/BZR1 (21-104) in complex with...

ID or keywords:

Entry

Database: PDB / ID: 9m73

Title

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

Components

E-box(CATATG)-containing DNA
Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

Keywords

DNA BINDING PROTEIN / Plant-specific / DNA-biding protein / Transcription factor / BZR

Function / homology

Function and homology information

plant ovule development / seed development / brassinosteroid mediated signaling pathway / cell envelope / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.31 Å

Authors

Shohei, N. / Masaru, T. / Takuya, M.

Funding support

Japan, 6items

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

Citation

Journal: Febs Lett. / Year: 2025
Title: Single cis-elements in brassinosteroid-induced upregulated genes are insufficient to recruit both redox states of the BIL1/BZR1 DNA-binding domain.
Authors: Nosaki, S. / Ohtsuka, M. / Nakano, T. / Tanokura, M. / Miyakawa, T.

History

Deposition	Mar 9, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 10, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9m73.cif.gz	855.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9m73.ent.gz	624.9 KB	Display	PDB format
PDBx/mmJSON format	9m73.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9m73_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	9m73_full_validation.pdf.gz	2 MB	Display
Data in XML	9m73_validation.xml.gz	74.7 KB	Display
Data in CIF	9m73_validation.cif.gz	96.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m7/9m73 ftp://data.pdbj.org/pub/pdb/validation_reports/m7/9m73	HTTPS FTP

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Related structure data

Related structure data	9m74C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (6) #221 - May 2018 Human Papillomavirus and Vaccines similarity (6) #90 - Jun 2007 Fatty Acid Synthase similarity (3) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (5) #100 - Apr 2008 Adrenergic Receptors similarity (1) #138 - Jun 2011 Glucansucrase similarity (1) #208 - Apr 2017 Glucose Transporters similarity (1) #74 - Feb 2006 alpha-Amylase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

C: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

D: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

G: E-box(CATATG)-containing DNA

H: E-box(CATATG)-containing DNA

A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

B: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

E: E-box(CATATG)-containing DNA

F: E-box(CATATG)-containing DNA

hetero molecules

219 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

D: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

G: E-box(CATATG)-containing DNA

H: E-box(CATATG)-containing DNA

hetero molecules

defined by author&software
Evidence: isothermal titration calorimetry
110 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

B: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1

E: E-box(CATATG)-containing DNA

F: E-box(CATATG)-containing DNA

hetero molecules

defined by author&software
Evidence: isothermal titration calorimetry
110 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.848, 92.602, 111.767
Angle α, β, γ (deg.)	90.000, 100.323, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein

Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1 / Protein BIN2 SUBSTRATE 2

Mass: 49819.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: malE, JW3994, BZR1, BIS2, At1g75080, F9E10.7 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P1LXE0, UniProt: Q8S307

#2: DNA chain

E-box(CATATG)-containing DNA

Mass: 4592.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

#3: Polysaccharide

alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose

#4: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

N

Has protein modification

N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.56 Å³/Da / Density % sol: 51.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50 mM sodium cacodylate pH 6.5, 200 mM potassium chloride, 10 mM magnesium chloride and 10% (w/v) polyethylene glycol (PEG) 4000

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Data collection

Diffraction	Mean temperature: 95 K / Ambient temp details: DECTRIS PILATUS 2M-F / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 19, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.31→43.62 Å / Num. obs: 90599 / % possible obs: 100 % / Redundancy: 7 % / B_iso Wilson estimate: 42.68 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.047 / Net I/σ(I): 16
Reflection shell	Resolution: 2.31→2.35 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4450 / CC_1/2: 0.746 / R_pim(I) all: 0.557 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.18_3855	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.31→43.62 Å / SU ML: 0.2828 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2451	4565	5.04 %
R_work	0.2054	85940	-
obs	0.2074	90505	99.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 59.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.31→43.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13584	1220	112	159	15075

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0058	15379
X-RAY DIFFRACTION	f_angle_d	0.6916	21116
X-RAY DIFFRACTION	f_chiral_restr	0.0453	2305
X-RAY DIFFRACTION	f_plane_restr	0.0041	2525
X-RAY DIFFRACTION	f_dihedral_angle_d	25.2685	5749

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.31-2.34	0.3407	126	0.2765	2869	X-RAY DIFFRACTION	99.9
2.34-2.36	0.3456	139	0.2783	2841	X-RAY DIFFRACTION	100
2.36-2.39	0.3179	142	0.2598	2889	X-RAY DIFFRACTION	100
2.39-2.42	0.2979	158	0.2545	2843	X-RAY DIFFRACTION	99.93
2.42-2.45	0.2882	152	0.2584	2860	X-RAY DIFFRACTION	100
2.45-2.49	0.3184	154	0.2581	2829	X-RAY DIFFRACTION	100
2.49-2.52	0.3066	141	0.2489	2861	X-RAY DIFFRACTION	100
2.52-2.56	0.3098	163	0.2486	2860	X-RAY DIFFRACTION	100
2.56-2.6	0.2693	187	0.2348	2822	X-RAY DIFFRACTION	100
2.6-2.64	0.2895	157	0.2317	2866	X-RAY DIFFRACTION	99.97
2.64-2.69	0.2672	158	0.2313	2821	X-RAY DIFFRACTION	100
2.69-2.74	0.2788	141	0.2379	2874	X-RAY DIFFRACTION	99.97
2.74-2.79	0.2982	153	0.2479	2870	X-RAY DIFFRACTION	99.93
2.79-2.85	0.3742	151	0.2617	2847	X-RAY DIFFRACTION	100
2.85-2.91	0.2696	151	0.2583	2844	X-RAY DIFFRACTION	100
2.91-2.98	0.3392	140	0.2447	2872	X-RAY DIFFRACTION	100
2.98-3.05	0.2803	164	0.2393	2868	X-RAY DIFFRACTION	100
3.05-3.13	0.291	133	0.2407	2874	X-RAY DIFFRACTION	99.9
3.14-3.23	0.2948	178	0.2468	2853	X-RAY DIFFRACTION	99.9
3.23-3.33	0.2981	146	0.2326	2841	X-RAY DIFFRACTION	99.9
3.33-3.45	0.2371	166	0.2179	2872	X-RAY DIFFRACTION	99.97
3.45-3.59	0.2389	140	0.2054	2867	X-RAY DIFFRACTION	100
3.59-3.75	0.2656	151	0.2043	2869	X-RAY DIFFRACTION	100
3.75-3.95	0.2269	121	0.1881	2924	X-RAY DIFFRACTION	99.93
3.95-4.2	0.2212	154	0.1665	2861	X-RAY DIFFRACTION	99.97
4.2-4.52	0.1852	168	0.1581	2858	X-RAY DIFFRACTION	99.9
4.52-4.97	0.1876	157	0.1519	2886	X-RAY DIFFRACTION	99.93
4.98-5.69	0.2082	157	0.1752	2890	X-RAY DIFFRACTION	99.77
5.69-7.17	0.2071	175	0.1902	2884	X-RAY DIFFRACTION	99.8
7.17-43.62	0.1685	142	0.166	2925	X-RAY DIFFRACTION	97.8

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.14114713681	-0.625460863467	-2.022091469	2.90926906802	0.420111202536	3.15523622811	0.184499202785	-0.256974481402	0.51245371863	-0.00270453873317	0.0325726968563	-0.187471724641	-0.327125489582	0.306979699615	-0.178040600995	0.371867652302	-0.0741434271673	0.0477806905087	0.260224843655	0.0136720702765	0.284414990616	-2.57090701659	14.2330538607	11.4420975675
2	4.90462819306	-1.62787787619	0.833351209034	4.75563783394	-1.24888701266	3.48353176001	-0.00383965421563	-0.370195606995	-0.754411373985	0.466773146967	0.104413706559	-0.049353001197	0.923850050888	-0.19506701946	-0.0865983137666	0.611085039695	-0.0903866330332	-0.0368850421714	0.292591829024	-0.00877415104781	0.418142442404	-6.38720904937	-37.0133727287	27.6808195299
3	1.3618731531	0.287782156283	-0.101285576125	3.12845324772	0.614541454772	2.76117702664	-0.193783883896	-0.188872388184	0.0664849324511	0.524331897359	0.639658632081	-0.730331560949	-0.293564736412	0.573043779139	-0.418519005953	0.567778086131	0.15516301954	-0.0571024526877	0.718152828454	-0.249340187071	0.464399986349	-8.67059843381	13.6381824217	45.3018114572
4	3.81967319155	1.47196797981	0.541046256779	3.47483417939	1.4163476257	2.988055955	-0.0350874631403	0.226701562466	-0.630401765573	-0.397906299172	0.124915390031	0.0441796577313	0.807819947543	-0.20926289731	-0.0679118633341	0.649586549783	-0.0662752331539	-0.0634444617746	0.254316135512	0.0413566463569	0.444513139242	-1.96712018335	-36.8855643944	25.6342343889
5	1.86870641803	-0.437934117499	0.647627075672	2.92803048116	-1.8582492181	9.33323810618	0.384495833761	-0.482918627326	-0.210242198516	0.537635753227	0.189774200608	-0.0206465964214	-0.116069358274	-0.400839409597	-0.549286309869	0.421408065627	-0.15075162704	-0.00783202098197	0.403111395902	0.00603843884528	0.338354140716	-5.88963661978	-23.8702358588	28.6158245743
6	3.72727380132	-0.532827416541	-3.47142100009	3.68624722397	1.8771048563	3.7529937306	0.53230871417	0.259168186257	-0.0354469509158	0.0518007524222	0.0261569404416	-0.263768924586	-0.664618820941	-0.117214974896	-0.524283442722	0.459599213073	-0.0315361263088	-0.0479418758794	0.361441274013	0.0150818274344	0.297286545768	-2.91458474868	-23.8239872067	24.7228946266
7	4.56085668406	0.367641221678	-1.37508591425	1.26734581036	-0.262419344557	1.69714915442	0.081672810349	-0.559268388799	-0.0422668682556	0.121117835251	-0.13927642741	-0.102461501604	0.0391399758943	0.640203103567	0.0528748006958	0.331127163877	0.0429112729512	0.00610343878234	0.5192861338	0.0135815159911	0.160858521216	39.8584413002	-13.1448796376	43.8982211553
8	1.16786749976	-2.00605260084	1.0295623002	7.52627661793	-6.03493741923	5.24854664949	-0.0213707757904	-0.104569643305	0.0809144416018	0.0905102697214	0.15016668576	0.486525677708	-0.234148048953	-0.541111877998	-0.130032070837	0.660257957635	-0.0606060203511	-0.0612977801401	0.700989210304	-0.24521982872	0.45431603534	45.7941368647	29.8545136678	29.9040777436
9	3.44205450061	-0.17912586478	-0.339768755239	1.3562606552	-0.217908327278	1.80342175351	-0.0548860124136	0.0853400552435	-0.0450109647794	-0.0592092747642	0.0372295629611	0.127704851399	0.0434940739175	-0.415346900204	0.0205322631554	0.293779041624	-0.0472261417202	0.0108031147107	0.307958591615	-0.00635083110319	0.149257607139	53.2703451938	-15.1309637792	11.0775701908
10	0.818868435883	0.75265432143	0.0938916626233	5.88548511014	2.7765949071	1.30584253488	-0.107428214853	-0.291956640064	-0.0315806243654	0.761744984606	0.272428258962	-0.372687600379	0.230810401065	0.405368840612	-0.186470686442	0.729855464902	0.175559742299	-0.109847487586	0.700738097837	0.0928605142627	0.439907439349	47.3531268501	29.9025926834	24.7359314966
11	0.21103400547	0.054355757025	0.916712944832	1.31377137741	2.16922264916	6.71815819504	0.316800973761	-0.440429312171	-0.067086253163	0.36218882832	0.218503385167	0.117401595183	2.55328634522	-0.712393419471	-0.476273297119	1.07784207163	0.00525712560095	-0.0693030134096	1.1832648755	0.0677215435832	0.416648686942	46.9881229251	23.6564891722	29.809453598
12	0.725154337016	0.723903819	-1.12541920156	1.0722025563	-2.69841560453	8.58474726796	0.207194648942	-0.715828092751	-0.0554184318996	0.240751254276	0.237999408348	-0.205921767131	2.28609717349	1.26331622197	-0.418642873564	1.22080291136	0.212989727205	-0.00438382583096	1.20244845749	0.0295303099273	0.445948457803	45.3762012713	23.5392391237	25.5664565524

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'C' and (resid -347 through 26 )	C	A	-347 - 26	1 - 374
2	2	chain 'C' and (resid 27 through 88 )	C	A	27 - 88	375 - 436
3	3	chain 'D' and (resid -347 through 26 )	D	D	-347 - 26	1 - 374
4	4	chain 'D' and (resid 27 through 88 )	D	D	27 - 88	375 - 436
5	5	chain 'G' and (resid -3 through 11 )	G	F	-3 - 11
6	6	chain 'H' and (resid -3 through 11 )	H	G	-3 - 11
7	7	chain 'A' and (resid -348 through 3 )	A	H	-348 - 3	1 - 352
8	8	chain 'A' and (resid 4 through 88 )	A	H	4 - 88	353 - 437
9	9	chain 'B' and (resid -347 through 4 )	B	K	-347 - 4	1 - 352
10	10	chain 'B' and (resid 5 through 88 )	B	K	5 - 88	353 - 436
11	11	chain 'E' and (resid -3 through 11 )	E	P	-3 - 11
12	12	chain 'F' and (resid -3 through 11 )	F	Q	-3 - 11

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