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- PDB-7vn2: Crystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7vn2
TitleCrystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with double-stranded DNA contaning ATCACGTGAT
Components
  • DNA (5'-D(*TP*TP*AP*TP*CP*AP*CP*GP*TP*GP*AP*TP*AP*AP*A)-3')
  • Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
KeywordsTRANSCRIPTION / Transcription factor-DNA complex
Function / homology
Function and homology information


plant ovule development / seed development / brassinosteroid mediated signaling pathway / carbohydrate transmembrane transporter activity / periplasmic space / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding ...plant ovule development / seed development / brassinosteroid mediated signaling pathway / carbohydrate transmembrane transporter activity / periplasmic space / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / DNA 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 speciesSerratia sp. (bacteria)
Arabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsNosaki, S. / Tanokura, M. / Miyakawa, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H05835, 19H04855, 19K23658, 21H02114 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101077 Japan
CitationJournal: Nat.Plants / Year: 2022
Title: Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout.
Authors: Nosaki, S. / Mitsuda, N. / Sakamoto, S. / Kusubayashi, K. / Yamagami, A. / Xu, Y. / Bui, T.B.C. / Terada, T. / Miura, K. / Nakano, T. / Tanokura, M. / Miyakawa, T.
History
DepositionOct 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,95710
Polymers106,0244
Non-polymers9336
Water77543
1
C: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
G: DNA (5'-D(*TP*TP*AP*TP*CP*AP*CP*GP*TP*GP*AP*TP*AP*AP*A)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)106,95710
Polymers106,0244
Non-polymers9336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9820 Å2
ΔGint-13 kcal/mol
Surface area41120 Å2
MethodPISA
2
A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
E: DNA (5'-D(*TP*TP*AP*TP*CP*AP*CP*GP*TP*GP*AP*TP*AP*AP*A)-3')
hetero molecules

A: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
E: DNA (5'-D(*TP*TP*AP*TP*CP*AP*CP*GP*TP*GP*AP*TP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,95710
Polymers106,0244
Non-polymers9336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9020 Å2
ΔGint-17 kcal/mol
Surface area42070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.596, 94.206, 102.340
Angle α, β, γ (deg.)90.000, 100.590, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 48419.836 Da / Num. of mol.: 2 / Mutation: D82A,K83A,E172A,N173A,K239A,E359A,K362A,D363A
Source method: isolated from a genetically manipulated source
Details: The fused Maltose binding protein is derived from Escherichia coli O157:H7
Source: (gene. exp.) Serratia sp. (strain FS14) (bacteria), (gene. exp.) Arabidopsis thaliana (thale cress)
Strain: FS14 / 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*AP*TP*CP*AP*CP*GP*TP*GP*AP*TP*AP*AP*A)-3')


Mass: 4592.022 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) 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.: 2
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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
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

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: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→45.11 Å / Num. obs: 39829 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 45.61 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.6
Reflection shellResolution: 2.42→2.51 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4191 / CC1/2: 0.881

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZD4

5zd4


Resolution: 2.42→35.87 Å / SU ML: 0.341 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.8134
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 1997 5.02 %
Rwork0.2228 37811 -
obs0.224 39808 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.57 Å2
Refinement stepCycle: LAST / Resolution: 2.42→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6796 610 62 43 7511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01227698
X-RAY DIFFRACTIONf_angle_d1.007710566
X-RAY DIFFRACTIONf_chiral_restr0.08511153
X-RAY DIFFRACTIONf_plane_restr0.00621263
X-RAY DIFFRACTIONf_dihedral_angle_d24.98312878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.480.3461340.30622734X-RAY DIFFRACTION99.9
2.48-2.550.34621360.29932711X-RAY DIFFRACTION99.79
2.55-2.620.31321660.28982722X-RAY DIFFRACTION99.93
2.62-2.710.28821690.27732634X-RAY DIFFRACTION99.86
2.71-2.80.30661500.27942698X-RAY DIFFRACTION99.75
2.8-2.920.29991310.29322751X-RAY DIFFRACTION99.9
2.92-3.050.29931660.28122680X-RAY DIFFRACTION99.72
3.05-3.210.31521560.26312686X-RAY DIFFRACTION99.68
3.21-3.410.29541280.24382716X-RAY DIFFRACTION99.41
3.41-3.670.25071330.24072702X-RAY DIFFRACTION98.75
3.67-4.040.24061290.20572723X-RAY DIFFRACTION98.75
4.04-4.630.19561250.17942688X-RAY DIFFRACTION97.88
4.63-5.820.19491410.17742677X-RAY DIFFRACTION97.64
5.82-35.870.18861330.16952689X-RAY DIFFRACTION95.76
Refinement TLS params.

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

IDL11 (°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)
12.968326581320.0528826347533-0.3494148440011.504947877630.4312306407193.807576474170.0319667828753-0.191766208057-0.3191657994810.0239794043403-0.006519548733310.01668685251180.07588061757820.190290757465-0.03031353237610.179046010498-0.02580982537550.0006947284372740.238313352910.04327055641510.375067309855-16.9450722596-13.7788490006-0.363048889368
22.275431499260.7607815220730.04684839073783.866525614530.7127328029132.20035816994-0.270273664399-0.05558173746220.9635154665330.02411287046350.1653733214280.0383731724448-0.3087078128770.2170931223340.1117943344970.3268980448940.0274100764956-0.07214896895450.233849056099-0.0008395431912980.6181524272841.4398157919337.6102908137-1.95181415453
34.433411426841.509952391661.233984741490.5136546074440.5520067827880.565185937908-0.5089922784340.611631117110.259445664167-0.04764158043750.3091324369-0.0351591442871-0.0122684386292-0.01449727693770.1618076023120.262999867048-0.0170801157481-0.00728285400140.2667475487530.05372105355480.4164017754332.0367528471724.5900881895-1.2405295448
42.13578900711-0.4922141840360.2908313623622.92936158158-0.06192846665413.06949087033-0.000799574319444-0.88564924950.17487524027-0.279114583939-0.1433879300610.3979369117380.0517701506538-1.210696128880.1680898565820.3275042185850.09634435014370.03378283203530.902903033165-0.2206491701920.4123235248093.5488319989212.255335435631.3393139187
51.97357681010.8440912184070.2073639439271.174319962141.346453722254.493704683870.0683577857856-1.234413596550.283531740240.254818686725-0.6406359811190.04872961411330.110821675023-1.134306381490.4112690348720.3260103716430.01751574363840.04552696636591.31185796858-0.305775717840.4339756078039.369642718415.318794174851.6237012563
61.463287308181.88104006114-0.6174127942474.061379311820.5578918301132.93698176637-0.1309635536020.301571503063-0.285951459818-0.1981827533780.280498420310.395139785723-0.1350446205320.0142877478886-0.1632930097330.4636567411970.0930110009793-0.1172175110950.757146627540.08048832968960.860933855145-7.16904249051-28.757624436750.3026309855
75.08803137167-2.293420724711.255033991691.00405866032-0.4428031253260.667937836443-0.3130574508190.1923056483250.918373147952-0.0102494510637-0.308288305416-0.137794364371-0.2818554378740.05448524104870.6136050923580.489260636086-0.0138781239509-0.07401578884841.321431177930.0708241726950.907349724065-7.829283632-23.338738564151.4813821151
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 'G' and (resid -3 through 11 )GC-3 - 11
44chain 'A' and (resid -347 through -266 )AD-347 - -2661 - 82
55chain 'A' and (resid -265 through 3 )AD-265 - 383 - 351
66chain 'A' and (resid 4 through 88 )AD4 - 88352 - 436
77chain 'E' and (resid -3 through 11 )EF-3 - 11

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