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- PDB-9m74: Crystal structure of MBP-fused BIL1/BZR1 (21-104) in complex with... -

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Basic information

Entry
Database: PDB / ID: 9m74
TitleCrystal structure of MBP-fused BIL1/BZR1 (21-104) in complex with double-stranded DNA contaning CACAGCTGTG
Components
  • DNA (5'-D(*TP*TP*CP*AP*CP*AP*GP*CP*TP*GP*TP*GP*AP*AP*A)-3')
  • Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
KeywordsDNA 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 ...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 / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
BZR family / BES1/BZR1 plant transcription factor, N-terminal / BES1/BZR1 plant transcription factor, N-terminal / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
alpha-maltose / DNA / DNA (> 10) / Maltodextrin-binding protein / Protein BRASSINAZOLE-RESISTANT 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsShohei, N. / Masaru, T. / Takuya, M.
Funding support Japan, 6items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H04855 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H04855 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19K23658 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)21H02114 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101077 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121010 Japan
CitationJournal: 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
DepositionMar 9, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
D: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
G: DNA (5'-D(*TP*TP*CP*AP*CP*AP*GP*CP*TP*GP*TP*GP*AP*AP*A)-3')
H: DNA (5'-D(*TP*TP*CP*AP*CP*AP*GP*CP*TP*GP*TP*GP*AP*AP*A)-3')
A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
B: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
E: DNA (5'-D(*TP*TP*CP*AP*CP*AP*GP*CP*TP*GP*TP*GP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*CP*AP*CP*AP*GP*CP*TP*GP*TP*GP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,20515
Polymers217,6508
Non-polymers1,5557
Water3,333185
1
C: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
D: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
G: DNA (5'-D(*TP*TP*CP*AP*CP*AP*GP*CP*TP*GP*TP*GP*AP*AP*A)-3')
H: DNA (5'-D(*TP*TP*CP*AP*CP*AP*GP*CP*TP*GP*TP*GP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5727
Polymers108,8254
Non-polymers7473
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-18 kcal/mol
Surface area40900 Å2
MethodPISA
2
A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
B: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
E: DNA (5'-D(*TP*TP*CP*AP*CP*AP*GP*CP*TP*GP*TP*GP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*CP*AP*CP*AP*GP*CP*TP*GP*TP*GP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6348
Polymers108,8254
Non-polymers8094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-6 kcal/mol
Surface area41340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.840, 92.506, 111.736
Angle α, β, γ (deg.)90.000, 100.167, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#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
DNA (5'-D(*TP*TP*CP*AP*CP*AP*GP*CP*TP*GP*TP*GP*AP*AP*A)-3')


Mass: 4593.011 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
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM sodium cacodylate pH 6.5, 200 mM ammonium acetate and 10 mM calcium chloride and 10% (w/v) polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→47.27 Å / Num. obs: 100538 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 39.6 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.045 / Net I/σ(I): 16.7
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4938 / CC1/2: 0.705 / Rpim(I) all: 0.568 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→43.58 Å / SU ML: 0.2781 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2067
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2438 5003 4.98 %
Rwork0.2151 95449 -
obs0.2165 100452 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.91 Å2
Refinement stepCycle: LAST / Resolution: 2.23→43.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13592 1220 104 185 15101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005415381
X-RAY DIFFRACTIONf_angle_d0.661921122
X-RAY DIFFRACTIONf_chiral_restr0.04442306
X-RAY DIFFRACTIONf_plane_restr0.00352526
X-RAY DIFFRACTIONf_dihedral_angle_d24.12765831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.260.32131770.30183155X-RAY DIFFRACTION99.97
2.26-2.280.37251790.29423139X-RAY DIFFRACTION99.97
2.28-2.310.31381760.27943149X-RAY DIFFRACTION100
2.31-2.340.27381920.27493163X-RAY DIFFRACTION99.94
2.34-2.370.32141430.26823169X-RAY DIFFRACTION99.97
2.37-2.40.27681670.27293154X-RAY DIFFRACTION99.97
2.4-2.440.33311460.27733197X-RAY DIFFRACTION99.97
2.44-2.470.34021410.28133189X-RAY DIFFRACTION99.97
2.47-2.510.29351750.27263202X-RAY DIFFRACTION100
2.51-2.550.34621710.27283148X-RAY DIFFRACTION100
2.55-2.60.33651540.2693201X-RAY DIFFRACTION100
2.6-2.640.30171290.25243217X-RAY DIFFRACTION100
2.64-2.690.30081450.24663157X-RAY DIFFRACTION99.97
2.69-2.750.27041640.25133173X-RAY DIFFRACTION99.97
2.75-2.810.31271330.26113232X-RAY DIFFRACTION99.97
2.81-2.870.29562100.25853127X-RAY DIFFRACTION99.97
2.87-2.950.30821610.27033179X-RAY DIFFRACTION99.94
2.95-3.030.30551870.27013171X-RAY DIFFRACTION99.97
3.03-3.120.34251560.26883175X-RAY DIFFRACTION100
3.12-3.220.25991670.25773204X-RAY DIFFRACTION99.94
3.22-3.330.25641710.23063131X-RAY DIFFRACTION99.82
3.33-3.460.24131720.21083209X-RAY DIFFRACTION99.91
3.46-3.620.24281560.20963192X-RAY DIFFRACTION99.97
3.62-3.810.24711800.19973166X-RAY DIFFRACTION99.97
3.81-4.050.22051760.18153204X-RAY DIFFRACTION99.88
4.05-4.360.20221680.16253163X-RAY DIFFRACTION99.97
4.36-4.80.18061700.15553215X-RAY DIFFRACTION99.91
4.8-5.50.17491860.16583200X-RAY DIFFRACTION99.97
5.5-6.920.19251730.18693241X-RAY DIFFRACTION99.82
6.92-43.580.17451780.16513227X-RAY DIFFRACTION98.41
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.15686444371-0.796793777005-2.236088548792.991599329870.5176283334363.13011537830.167319645523-0.2876956301030.4309262722980.002008224891310.0538728270389-0.185951776029-0.3003534665620.304321435879-0.1754378552340.31536514197-0.06989060663420.02578580793360.2769094773820.00233435188360.252387031098-2.628497137814.251249825111.4518679759
25.31723164302-1.564872252090.4686494698664.91173415786-1.383752646624.43090318375-0.00460026671135-0.428796651294-0.7754389156060.448992799520.0770174301719-0.1715613474950.936982799737-0.0332344628388-0.05968708183720.523865956231-0.0540092661982-0.04942521743270.3061658103530.00719730948630.445059259377-6.36184406867-36.884606278427.7305277976
32.48135617237-0.371838601903-0.1204075621070.655591321679-0.1450994838470.749461381482-0.286501207512-0.3397832625440.3312073685760.4914906922370.689561870972-0.887481346454-0.0554629576010.838952271202-0.4611458140530.8104952944020.213973815632-0.2132985997891.12436130403-0.5468837355510.9212352876374.683504625913.531748818945.5862408669
41.061315187680.312924373009-0.2884076396523.010844822040.7062211715072.32992084528-0.179065918002-0.2010523107080.08732809128130.6624299561320.527593789822-0.296111026972-0.2717600470480.222072440174-0.280560465030.5572502502710.212889408821-0.03124382123760.656097691403-0.1023940578190.34292097093-14.755838485513.785909297445.1112327458
50.5617364512210.0957065697859-0.1999181643020.18065817953-0.2097930439540.346395370781-0.05189824443190.144917463569-0.253727631063-0.09208267405040.0366793264910.2381990078470.667395038667-0.3191168281770.045416014340.609948723293-0.123424969396-0.03593466364160.379262911441-0.02828133109260.556990147156-2.02738393863-36.776234268325.563728759
60.103393170715-0.02956816088080.04906982345720.1595768929380.01105101040020.04986618921260.481688444114-0.5498888618460.02669446509380.5131883054320.0332971842144-0.0136679128298-0.286166190751-0.443166343123-0.4750778080140.908911699771-0.1127509821750.0515393857490.7754558020940.04125928891850.367631367424-5.83003968968-23.717603478828.610444104
70.366669816886-0.05399893329260.2525601067040.517603403967-0.2397898304150.359889618460.273899585126-0.1134105562570.08203164084610.240260359077-0.0501540601636-0.109846345446-0.34333173095-0.0268398222424-0.06070668848210.6528078630940.01973665092640.04344118787550.515986686012-0.01414743754430.289803808985-2.90946846536-23.689384433724.7832599386
83.186190813920.215581264184-1.003207375380.996860410014-0.008396387837241.7648879830.0800025126697-0.429236434128-0.05168998565660.0732653645588-0.0909118991142-0.0478004660115-0.002590423538430.436832480082-0.03750102811110.2959954775250.0189146955043-0.01711721667270.392202414210.01245105200460.13449922584539.8875059734-13.295305106643.8752687807
91.192336003170.4972189995981.122248708670.2974603223030.4179603599561.05141731128-0.03226370628710.1996982524050.203005096687-0.609755257040.3239641601160.250439644861-0.155327648761-0.195739696584-0.4603903462870.662100898693-0.248773699602-0.000782079427190.6865126784140.02177593195340.4072905784249.134064928.4371188566744.0084193279
100.739360725461-0.3498484048330.1570373031150.7334148293910.7558668926041.257288919450.068025330697-0.3800553693060.06077401017690.0457337959165-0.0810936761412-0.182495380760.03200399593570.0326830582220.01629990185840.6462411142620.0253533780755-0.150996780430.630560697698-0.01121887078990.57112044322944.962509600136.396893924125.3154732866
112.74282849919-0.0956922850007-0.3175526427521.06220257423-0.5071893682992.06064239483-0.04175504645470.08635117776350.0921268249722-0.05275734459080.0779962126420.0721109535149-0.0528928275682-0.284459911804-0.05968987393790.261821791721-0.0229208217356-0.007893109642680.219994848736-0.0145446584950.16026298171152.7768465432-14.080617327111.068956917
120.2526074242740.29225315971-0.003157980034560.208874821225-0.1564606497410.1704153057860.06955321916870.265840604793-0.109864712440.15308423037-0.1252677128790.18201432908-0.04510326569980.1201057767960.1243503614510.6918190126870.0994226767151-0.1460188158490.648810923767-0.01217715512670.62267117806448.817729248836.72568432828.6852289142
130.557732561335-0.1092354704720.7705092438622.130608921683.360508524374.929397084770.443509790268-0.196651079501-0.431316007883-0.101623144579-0.1007008652730.5653557619770.669636144184-0.4235460667260.1126714438940.6850546185050.08950782163660.01053685578430.9732775790350.01335105316680.36251175105247.068589011723.552606847529.8491834792
140.285400405677-0.05122836750520.6426977754880.622888184822-2.916839908687.856142931670.613998549603-1.2253946098-1.350227653721.30251638650.413601897339-2.498083621940.5667468397480.7083911270450.0267107003390.663958289111-0.007726201364590.4222556876140.8017711252840.305774919664-4.1332886829545.443499780323.493511682725.5937811335
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid -348 through 26 )CA-348 - 261 - 375
22chain 'C' and (resid 27 through 88 )CA27 - 88376 - 437
33chain 'D' and (resid -347 through -230 )DD-347 - -2301 - 118
44chain 'D' and (resid -229 through 26 )DD-229 - 26119 - 374
55chain 'D' and (resid 27 through 88 )DD27 - 88375 - 436
66chain 'G' and (resid -3 through 11 )GF-3 - 11
77chain 'H' and (resid -3 through 11 )HG-3 - 11
88chain 'A' and (resid -348 through 3 )AH-348 - 31 - 352
99chain 'A' and (resid 4 through 26 )AH4 - 26353 - 375
1010chain 'A' and (resid 27 through 88 )AH27 - 88376 - 437
1111chain 'B' and (resid -347 through 26 )BK-347 - 261 - 374
1212chain 'B' and (resid 27 through 88 )BK27 - 88375 - 436
1313chain 'E' and (resid -3 through 11 )EN-3 - 11
1414chain 'F' and (resid -3 through 11 )FO-3 - 11

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