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- PDB-2lex: Complex of the C-terminal WRKY domain of AtWRKY4 and a W-box DNA -

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Basic information

Entry
Database: PDB / ID: 2lex
TitleComplex of the C-terminal WRKY domain of AtWRKY4 and a W-box DNA
Components
  • DNA (5'-D(*CP*G*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*GP*C)-3')
  • DNA (5'-D(*GP*CP*GP*C*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*CP*G)-3')
  • Probable WRKY transcription factor 4
KeywordsTRANSCRIPTION/DNA / transcription / TRANSCRIPTION-DNA complex / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of defense response to fungus / negative regulation of defense response to bacterium / response to ethylene / response to salicylic acid / response to jasmonic acid / defense response / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA binding ...regulation of defense response to fungus / negative regulation of defense response to bacterium / response to ethylene / response to salicylic acid / response to jasmonic acid / defense response / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA binding / metal ion binding / nucleus
Similarity search - Function
WRKY domain / WRKY transcription factor, plant / WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain / N-terminal domain of TfIIb / Single Sheet / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Probable WRKY transcription factor 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYamasaki, K. / Kigawa, T. / Watanabe, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for sequence-spscific DNA recognition by an Arabidopsis WRKY transcription factor
Authors: Yamasaki, K. / Kigawa, T. / Watanabe, S. / Inoue, M. / Yamasaki, T. / Seki, M. / Shinozaki, K. / Yokoyama, S.
History
DepositionJun 24, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable WRKY transcription factor 4
B: DNA (5'-D(*CP*G*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*GP*C)-3')
C: DNA (5'-D(*GP*CP*GP*C*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4524
Polymers18,3873
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Probable WRKY transcription factor 4 / WRKY DNA-binding protein 4


Mass: 8587.530 Da / Num. of mol.: 1 / Fragment: WRKY domain, residues 399-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WRKY4 / Production host: cell free synthesis (unknown) / References: UniProt: Q9XI90
#2: DNA chain DNA (5'-D(*CP*G*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*GP*C)-3')


Mass: 4835.130 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*GP*CP*GP*C*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*CP*G)-3')


Mass: 4964.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY
1422D 1H-15N HSQC
1523D HNCA
1623D HN(CO)CA
1723D HN(CA)CB
1823D CBCA(CO)NH
1923D 1H-15N NOESY
11023D 1H-15N TOCSY
21132D 1H-15N HSQC
31242D 1H-15N HSQC
31342D 1H-15N IPAP-HSQC
31452D 1H-15N HSQC
31552D 1H-15N IPAP-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4-1.0 mM WRKY domain-1, 0.4-1.0 mM W-box DNA chain 1-2, 0.4-1.0 mM W-box DNA chain 2-3, 20 mM potassium phosphate-4, 200 mM potassium chloride-5, 20 uM zinc chloride-6, 1 mM [U-2H] DTT-7, 50 uM DSS-8, 95% H2O/5% D2O95% H2O/5% D2O
20.4-1.0 mM [U-13C; U-15N] WRKY domain-9, 0.4-1.0 mM W-box DNA chain 1-10, 0.4-1.0 mM W-box DNA chain 2-11, 20 mM potassium phosphate-12, 200 mM potassium chloride-13, 20 uM zinc chloride-14, 1 mM [U-2H] DTT-15, 50 uM DSS-16, 95% H2O/5% D2O95% H2O/5% D2O
30.4-1.0 mM [U-13C; U-15N] WRKY domain-17, 0.4-1.0 mM W-box DNA chain 1-18, 0.4-1.0 mM W-box DNA chain 2-19, 20 mM potassium phosphate-20, 200 mM potassium chloride-21, 20 uM zinc chloride-22, 1 mM [U-2H] DTT-23, 50 uM DSS-24, 100% D2O100% D2O
40.4-1.0 mM [U-15N] WRKY domain-25, 0.4-1.0 mM [U-15N]-T W-box DNA chain 1-26, 0.4-1.0 mM [U-15N]-T W-box DNA chain 2-27, 20 mM potassium phosphate-28, 200 mM potassium chloride-29, 20 uM zinc chloride-30, 1 mM [U-2H] DTT-31, 50 uM DSS-32, 95% H2O/5% D2O95% H2O/5% D2O
50.4-1.0 mM [U-15N] WRKY domain-33, 0.4-1.0 mM [U-15N]-T W-box DNA chain 1-34, 0.4-1.0 mM [U-15N]-T W-box DNA chain 2-35, 20 mM potassium phosphate-36, 200 mM potassium chloride-37, 20 uM zinc chloride-38, 1 mM [U-2H] DTT-39, 50 uM DSS-40, 12 mg/mL Pf1 phage-41, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMWRKY domain-10.4-1.01
mMW-box DNA chain 1-20.4-1.01
mMW-box DNA chain 2-30.4-1.01
20 mMpotassium phosphate-41
200 mMpotassium chloride-51
20 uMzinc chloride-61
1 mMDTT-7[U-2H]1
50 uMDSS-81
mMWRKY domain-9[U-13C; U-15N]0.4-1.02
mMW-box DNA chain 1-100.4-1.02
mMW-box DNA chain 2-110.4-1.02
20 mMpotassium phosphate-122
200 mMpotassium chloride-132
20 uMzinc chloride-142
1 mMDTT-15[U-2H]2
50 uMDSS-162
mMWRKY domain-17[U-13C; U-15N]0.4-1.03
mMW-box DNA chain 1-180.4-1.03
mMW-box DNA chain 2-190.4-1.03
20 mMpotassium phosphate-203
200 mMpotassium chloride-213
20 uMzinc chloride-223
1 mMDTT-23[U-2H]3
50 uMDSS-243
mMWRKY domain-25[U-15N]0.4-1.04
mMW-box DNA chain 1-26[U-15N]-T0.4-1.04
mMW-box DNA chain 2-27[U-15N]-T0.4-1.04
20 mMpotassium phosphate-284
200 mMpotassium chloride-294
20 uMzinc chloride-304
1 mMDTT-31[U-2H]4
50 uMDSS-324
mMWRKY domain-33[U-15N]0.4-1.05
mMW-box DNA chain 1-34[U-15N]-T0.4-1.05
mMW-box DNA chain 2-35[U-15N]-T0.4-1.05
20 mMpotassium phosphate-365
200 mMpotassium chloride-375
20 uMzinc chloride-385
1 mMDTT-39[U-2H]5
50 uMDSS-405
12 mg/mLPf1 phage-415
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1200 6.0 ambient 303 K
2200 6.0 ambient 283 K
3200 6.0 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Felix2000Accelrys Software Inc.data analysis
TALOS+Shen, Delaglio, Cornilescu, Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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