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- PDB-7vn3: Crystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7vn3
TitleCrystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with double-stranded DNA contaning CACACGTGTG
Components
  • DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*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: 1.94 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
D: Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1
G: DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
H: DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*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*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,85519
Polymers212,0518
Non-polymers1,80411
Water8,251458
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*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
H: DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,95910
Polymers106,0264
Non-polymers9336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-3 kcal/mol
Surface area40460 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*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8969
Polymers106,0264
Non-polymers8715
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-17 kcal/mol
Surface area41150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.656, 92.905, 111.935
Angle α, β, γ (deg.)90.000, 100.333, 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: 48419.836 Da / Num. of mol.: 4 / 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*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3')


Mass: 4593.011 Da / Num. of mol.: 4 / 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.: 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
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: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→47.37 Å / Num. obs: 152181 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 1.94→1.97 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7525 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
XDS1.18_3855data reduction
PHENIX1.18_3855refinement
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZD4
Resolution: 1.94→35.5 Å / SU ML: 0.2162 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2307 7618 5.01 %
Rwork0.2018 144466 -
obs0.2032 152084 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.78 Å2
Refinement stepCycle: LAST / Resolution: 1.94→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13592 1220 120 458 15390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005215417
X-RAY DIFFRACTIONf_angle_d0.653121164
X-RAY DIFFRACTIONf_chiral_restr0.04682308
X-RAY DIFFRACTIONf_plane_restr0.00392532
X-RAY DIFFRACTIONf_dihedral_angle_d23.15125769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.960.30242440.27254776X-RAY DIFFRACTION99.92
1.96-1.990.27162540.26694804X-RAY DIFFRACTION99.92
1.99-2.010.29752590.274848X-RAY DIFFRACTION99.9
2.01-2.030.30682460.26884798X-RAY DIFFRACTION99.88
2.03-2.060.31382770.26474832X-RAY DIFFRACTION99.96
2.06-2.090.29662480.2524770X-RAY DIFFRACTION99.92
2.09-2.120.30432530.25324816X-RAY DIFFRACTION99.9
2.12-2.150.27332430.2414867X-RAY DIFFRACTION99.84
2.15-2.180.29042640.24014783X-RAY DIFFRACTION99.92
2.18-2.220.26442380.22954842X-RAY DIFFRACTION99.88
2.22-2.260.26932510.23544825X-RAY DIFFRACTION99.9
2.26-2.30.25892300.22944843X-RAY DIFFRACTION99.84
2.3-2.340.242540.23034847X-RAY DIFFRACTION99.8
2.34-2.390.24172550.2254815X-RAY DIFFRACTION99.84
2.39-2.440.24142540.22574809X-RAY DIFFRACTION99.74
2.44-2.50.2692600.23414832X-RAY DIFFRACTION99.84
2.5-2.560.28852640.23434794X-RAY DIFFRACTION99.78
2.56-2.630.24792730.22284830X-RAY DIFFRACTION99.84
2.63-2.710.24332780.21934774X-RAY DIFFRACTION99.72
2.71-2.80.24392520.2294830X-RAY DIFFRACTION99.76
2.8-2.90.27212640.22814813X-RAY DIFFRACTION99.67
2.9-3.010.27942670.23364823X-RAY DIFFRACTION99.45
3.01-3.150.27012340.22334791X-RAY DIFFRACTION98.88
3.15-3.320.22382710.21474832X-RAY DIFFRACTION99.09
3.32-3.520.2312690.19564733X-RAY DIFFRACTION98.68
3.52-3.80.2232470.18964836X-RAY DIFFRACTION99.03
3.8-4.180.19392360.16784824X-RAY DIFFRACTION98.6
4.18-4.780.16362520.15024798X-RAY DIFFRACTION98.54
4.78-6.020.18332430.16254831X-RAY DIFFRACTION98.24
6.02-35.50.18412380.164850X-RAY DIFFRACTION96.6
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)
14.4127032227-0.561087979939-1.547020906312.768248942160.3929492397012.845716649410.0844638817325-0.3845860889420.1260181763870.052153980977-0.04012962931630.0185786913124-0.2037366663020.224461877026-0.03168765695230.300942368337-0.05466427564610.03556342669850.2272700338340.02100704454780.191896643298-54.023126726614.003668631511.2994435446
23.53561440984-1.376498610320.3857190401273.25898585577-0.2510141171532.623026999120.0311417832013-0.328676358108-0.5792092960680.4875724065560.140369763013-0.1189992097090.890147923047-0.214598052415-0.1210191009710.544338086621-0.06510749749-0.0987633123960.2004719728120.01965823595060.35658667715-57.8333854777-37.104545366628.0219494989
30.7592450826950.2381551050610.8123086655331.677755549660.5069672234072.84875587128-0.3380522806840.0658621778143-0.01179767815750.6406435800590.64276365003-1.2697720205-0.002974978504820.816268162594-0.2943709763970.7126887208430.241860292916-0.3429351618541.11111131045-0.5273040483611.02279900387-44.412596046313.020998889644.6962518988
42.118907931530.415370478754-0.2235503961723.526555907310.508406652912.57525061552-0.143237818025-0.0207296002930.06610422701650.8231246329110.501986649645-0.306994564377-0.2955186329980.268413216814-0.3208109795840.5619301895310.18764736047-0.05429921224240.521248433119-0.106959596460.273166831452-65.612478220717.301471180144.7020995085
51.238704847130.107617362783-0.4285190593051.89705044186-0.6371939135041.33997150819-0.2981379637220.0216609988222-0.1342873331770.8868217622550.561050416007-0.421906503180.2358548866810.177596319281-0.2602351950830.5909988556530.27023975203-0.08941589493340.557614132855-0.1446688076830.400302146291-65.83831244123.3625606711345.8616874124
62.679432701471.793762539280.5464406157553.156291373551.010328131192.19846905320.05351804892090.161809349013-0.40515255026-0.05256413347860.1593837383280.005501933876160.866120231932-0.0918108365347-0.1715605748930.528648035162-0.0471714900098-0.11889697390.2120899826940.0365932920370.363568303664-53.5922847629-37.074369225325.8131728448
70.4836933666390.110621076680.6028857465133.20469830235-2.674270126377.510674105040.327155112485-0.120626099338-0.05608597090310.5223059472990.0970669964380.07413242250930.553399763306-0.909759955563-0.3909494564950.291528202216-0.136353931525-0.02473776204810.3293462327550.02468138792360.280611276292-57.4469450468-24.060729732728.8500822493
81.305338578970.2330620339630.01964447133773.175030517562.159342791262.96917487450.222413331148-0.211546989846-0.05019155631030.1799020718420.119579779324-0.3100461961270.3778841578070.176851065697-0.2518331786510.272984605288-0.0135247287793-0.05784755429630.2304514498530.009284525742590.233737362572-54.3200769093-24.064572774825.0145413538
93.728116882730.271103333101-0.9000255566551.10038727604-0.2245394770741.564330632610.112535048826-0.375391481220.07728491669830.107891699156-0.141231269558-0.0732845471577-0.01947200025450.5732027591450.02866640363820.2604229372110.00394397630168-0.01816719734060.41335144705-0.001949337336430.146504689312-11.6249020014-13.546412444343.8385611606
101.23909913767-1.325554502920.366589076316.40281972046-5.218508266684.60973726187-0.1004260189680.1562398474520.0816132939940.2664093206020.2457566918690.188082336957-0.515820021129-0.772369574751-0.11096097540.743348525614-0.104543936969-0.07126545305120.792081940196-0.209345457210.392548378084-5.6083347059429.330044320929.9235157824
113.66482794149-0.464229051574-0.6294166665581.32809808829-0.2764217287712.18386061449-0.009464207166410.2227175326670.0496670945937-0.07982833104780.05757231292250.1200138505190.022877216307-0.49307463288-0.03885261629460.234611593798-0.0289860598737-0.01098178409210.2669980445860.01023785465720.1554785571591.90829265785-15.459269571911.0254783414
121.607588308272.241975504820.8998347669886.993253342894.530598656823.200173359030.0707939995864-0.135985820606-0.0704832773780.3454262826960.153514632493-0.440128680977-0.2789876957760.477015649029-0.2065130641180.8100951936940.11289498546-0.0852664928260.745199630590.2296708803340.472440605712-4.4801354703228.688279338625.6154437053
130.0464896935049-0.165429763821-0.5518830198880.705293952062.336128848247.358989315380.0639042897449-0.018105674357-0.09505303303460.273317451540.191124910930.08491810692341.824593303160.0497089693916-0.2266036797930.8815578132470.0552635278151-0.06789152369650.9826657829810.04984398630930.385899772764-4.4906215988523.412978796929.8958193804
140.09958352312170.288275763805-0.8109488460250.861496215031-2.703820113888.528239848330.103922280165-0.409930547082-0.0745018308157-0.09851074130020.27617825209-0.09357800776682.0502041687-0.0198380335352-0.3291070181380.8798963247580.00283267523761-0.06831051484330.9271882387920.03702082601920.380635520074-6.0556445283623.367610458625.6853625621
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid -368 through 26 )CA-368 - 261 - 376
22chain 'C' and (resid 27 through 88 )CA27 - 88377 - 438
33chain 'D' and (resid -367 through -263 )DC-367 - -2631 - 105
44chain 'D' and (resid -262 through -54 )DC-262 - -54106 - 314
55chain 'D' and (resid -53 through 26 )DC-53 - 26315 - 374
66chain 'D' and (resid 27 through 88 )DC27 - 88375 - 436
77chain 'G' and (resid -3 through 11 )GE-3 - 11
88chain 'H' and (resid -3 through 11 )HF-3 - 11
99chain 'A' and (resid -368 through -17 )AG-368 - -171 - 353
1010chain 'A' and (resid -16 through 88 )AG-16 - 88354 - 438
1111chain 'B' and (resid -367 through -17 )BI-367 - -171 - 351
1212chain 'B' and (resid -16 through 88 )BI-16 - 88352 - 436
1313chain 'E' and (resid -3 through 11 )EK-3 - 11
1414chain 'F' and (resid -3 through 11 )FL-3 - 11

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