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- PDB-7z0u: Crystal structure of AtWRKY18 DNA-binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7z0u
TitleCrystal structure of AtWRKY18 DNA-binding domain in complex with W-box DNA
Components
  • DNA (5'-D(*CP*GP*CP*CP*TP*TP*GP*AP*CP*CP*AP*GP*CP*GP*C)-3')
  • DNA (5'-D(*GP*CP*GP*CP*TP*GP*GP*TP*CP*AP*AP*GP*GP*CP*G)-3')
  • WRKY transcription factor 18
KeywordsTRANSCRIPTION / transcription factor / DNA-binding domain / zinc binding
Function / homology
Function and homology information


regulation of defense response / response to salicylic acid / defense response to fungus / response to molecule of bacterial origin / sequence-specific DNA binding / defense response to bacterium / DNA-binding transcription factor activity / identical protein binding / nucleus
Similarity search - Function
WRKY transcription factor, plant / WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain
Similarity search - Domain/homology
DNA / DNA (> 10) / WRKY transcription factor 18
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGrzechowiak, M. / Jaskolski, M. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: New aspects of DNA recognition by group II WRKY transcription factor revealed by structural and functional study of AtWRKY18 DNA binding domain.
Authors: Grzechowiak, M. / Ruszkowska, A. / Sliwiak, J. / Urbanowicz, A. / Jaskolski, M. / Ruszkowski, M.
History
DepositionFeb 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Jan 31, 2024Group: 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
A: WRKY transcription factor 18
B: DNA (5'-D(*CP*GP*CP*CP*TP*TP*GP*AP*CP*CP*AP*GP*CP*GP*C)-3')
C: DNA (5'-D(*GP*CP*GP*CP*TP*GP*GP*TP*CP*AP*AP*GP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3804
Polymers18,3143
Non-polymers651
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-25 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.788, 112.788, 101.664
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein WRKY transcription factor 18 / WRKY DNA-binding protein 18 / AtWRKY18


Mass: 9132.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ...Details: MDGSSFLDISLDLNTNPFSAKLPKKEVSVLASTHLKRKWLEQDESASELREELNRVNSENKKLTEMLARVCESYNELHNHLEKLQSRQSPEIEQTDIPIKKRKQDPDEFLGFPIGLSSGKTENSSSNEDHHHHHQQHEQKNQLLSCKRPVTDSFNKAKVSTVYVPTETSDTSLTVKDGFQWRKYGQKVTRDNPSPRAYFRCSFAPSCPVKKKVQRSAEDPSLLVATYEGTHNHLGPNASEGDATSQGGSSTVTLDLVNGCHRLALEKNERDNTMQEVLIQQMASSLTKDSKFTAALAAAISGRLMEQSRT
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WRKY18, At4g31800, F28M20.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C5T4
#2: DNA chain DNA (5'-D(*CP*GP*CP*CP*TP*TP*GP*AP*CP*CP*AP*GP*CP*GP*C)-3')


Mass: 4530.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*GP*CP*TP*GP*GP*TP*CP*AP*AP*GP*GP*CP*G)-3')


Mass: 4651.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.41 Å3/Da / Density % sol: 72.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.03 M sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulfate, 0.1 M buffer system 1 (Imidazole; MES monohydrate (acid) ) pH 6.5, 20% v/v PEG 500* MME and 10 % w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.85→39.88 Å / Num. obs: 7918 / % possible obs: 97.6 % / Redundancy: 23.9 % / Biso Wilson estimate: 91.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.139 / Net I/σ(I): 21.03
Reflection shellResolution: 2.85→3.03 Å / Redundancy: 25.7 % / Rmerge(I) obs: 2.242 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1246 / CC1/2: 0.691 / % possible all: 69.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19_4092refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Z0R

7z0r


Resolution: 2.85→39.88 Å / SU ML: 0.5418 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.8776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2995 385 5 %
Rwork0.2508 7308 -
obs0.2533 7693 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.32 Å2
Refinement stepCycle: LAST / Resolution: 2.85→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms614 609 1 8 1232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063630
X-RAY DIFFRACTIONf_angle_d0.8363856
X-RAY DIFFRACTIONf_chiral_restr0.0509211
X-RAY DIFFRACTIONf_plane_restr0.0077141
X-RAY DIFFRACTIONf_dihedral_angle_d27.7586525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.270.46421280.38292434X-RAY DIFFRACTION99.3
3.27-4.110.36611210.32462286X-RAY DIFFRACTION92.15
4.12-39.880.24431360.19532588X-RAY DIFFRACTION99.93
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)
14.266915553642.91012116623-3.440738477625.0106679484-2.339196254164.348133437080.5900575653910.7730287037960.332869812570.13470969478-0.206645986845-0.786301725234-0.2826485965250.164325396116-0.2268959000330.4578192153230.109057337751-0.2363358484650.391149787238-0.01172298598770.97057665043230.528723441148.487818516433.728296351
20.8874950000881.641070362141.622783455033.932245420272.859564482473.00124475026-0.106483828264-0.5173197339190.9718892771350.00790439610797-0.7627720050170.6160562781650.0243625726355-0.2923188369190.6783461950660.4577277284180.104050726129-0.1827266354240.454488609069-0.05771076465021.000999627818.567441413753.045321500533.9989729961
31.05125472591-0.687828639657-0.4727556977120.453151005340.4081687742012.071695194270.269251017508-0.002247186903750.35731120193-0.08550366735180.164855817415-0.534970920475-0.387065016142-0.04845412227150.3862329519660.3771913690850.225380886772-0.121384343420.198477427186-0.04652955718521.0854838220521.604532887755.699697903722.1655091252
48.0169896022-0.05450126342827.680966824188.745439369963.183674838149.274189483690.1989697496651.902568226440.129241315449-0.3455614127980.966703704517-2.14444877609-0.05260853439411.18108260623-1.149138265070.5916765783-0.1480354806870.1394662895010.6085584629390.01862132875551.1213547607421.648327682339.512956330120.6128608229
53.08511829712-2.86825118625-0.7844052980852.742479843371.504541274968.000047751110.2970363237760.4397195718920.247852713306-0.4140508622240.382257501955-0.978878608003-1.301290133630.193131250438-0.5242824393160.4057962043590.1323866687970.03817531098730.247458070431-0.02016126224881.0219464360227.269206578759.684749793824.5303878068
60.95363992865-0.459039389290.04194785417950.689941851343-0.2145687375460.5595584306820.1322094076270.1068238764540.0798220989139-0.0497304068293-0.114143725563-0.1981137917260.153314387120.09692039037080.09827696574460.202838105660.241671652174-0.3222860548670.181851849168-0.04289572425491.2205088994925.114008328646.705686225929.7945360083
75.738691444032.58047881825-3.458929226814.8694547015-3.728297054863.35752581278-0.3317681086440.3675199982451.630893709970.3094392495350.6096889450110.256857232528-1.226010295260.96908818488-0.03445608761370.783708058682-0.229940518074-0.4511621239340.710444128574-0.09784759047681.5365152867734.124589295664.746273654732.2743295829
82.8197006473-2.73660073870.9620550614043.11376879123-1.86602614772.20955894483-0.01255236079520.819823937430.662366827817-0.892239185790.442415419883-1.199308107440.180688583480.590462959315-0.4169452665030.5949305613450.1035134476670.1394405914140.645810185128-0.2057452292521.4145434088223.077099856753.766637028812.5008656342
95.4524476453-2.83751043098-1.267077127347.250923160271.666078195084.342903971380.3918513775512.003921710560.0135884422385-1.32534912305-0.537589134022-0.664206615964-0.404575290014-0.356290288128-0.1139969322950.5632402579510.2284118212430.07356693338780.677578524153-0.1751028695471.1342968496320.93672820353.646485698511.2526903424
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 158 through 165 )AA158 - 1651 - 8
22chain 'A' and (resid 166 through 180 )AA166 - 1809 - 23
33chain 'A' and (resid 181 through 188 )AA181 - 18824 - 31
44chain 'A' and (resid 189 through 194 )AA189 - 19432 - 37
55chain 'A' and (resid 195 through 209 )AA195 - 20938 - 52
66chain 'A' and (resid 210 through 228 )AA210 - 22853 - 71
77chain 'A' and (resid 229 through 235 )AA229 - 23572 - 78
88chain 'B' and (resid 1 through 15 )BB1 - 15
99chain 'C' and (resid 1 through 15 )CC1 - 15

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