BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17732

Title: Complex of the C-terminal WRKY domain of AtWRKY4 and a W-box DNA   PubMed: 22219184

Authors: Kigawa, Takanori; Watanabe, Satoru; Inoue, Makoto; Yokoyama, Shigeyuki

Citation: Yamasaki, Kazuhiko; Kigawa, Takanori; Watanabe, Satoru; Inoue, Makoto; Yamasaki, Tomoko; Seki, Motoaki; Shinozaki, Kazuo; Yokoyama, Shigeyuki. "Structural Basis for Sequence-specific DNA Recognition by an Arabidopsis WRKY Transcription Factor."  J. Biol. Chem. 287, 7683-7691 (2012).

Assembly members:
WRKY_domain, polymer, 78 residues, 7208.253 Da.
ZN, non-polymer, 65.409 Da.
W-box_DNA_chain_1, polymer, . residues, Formula weight is not available
W-box_DNA_chain_2, polymer, . residues, Formula weight is not available

Natural source:   Common Name: thale-cress   Taxonomy ID: 3702   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Arabidopsis thaliana

Experimental source:   Production method: cell free synthesis   Host organism: E. coli - cell free

Entity Sequences (FASTA):
WRKY_domain: GSSGSSGVQTTSEVDLLDDG YRWRKYGQKVVKGNPYPRSY YKCTTPGCGVRKHVERAATD PKAVVTTYEGKHNHDLPA
W-box_DNA_chain_1: CGCCTTTGACCAGCGC
W-box_DNA_chain_2: GCGCTGGTCAAAGGCG

Data sets:
Data typeCount
13C chemical shifts70
15N chemical shifts80
1H chemical shifts662

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1WRKY_domain1
2ZINC_ION2
3W-box_DNA_chain_13
4W-box_DNA_chain_24

Entities:

Entity 1, WRKY_domain 78 residues - 7208.253 Da.

1   GLYSERSERGLYSERSERGLYVALGLNTHR
2   THRSERGLUVALASPLEULEUASPASPGLY
3   TYRARGTRPARGLYSTYRGLYGLNLYSVAL
4   VALLYSGLYASNPROTYRPROARGSERTYR
5   TYRLYSCYSTHRTHRPROGLYCYSGLYVAL
6   ARGLYSHISVALGLUARGALAALATHRASP
7   PROLYSALAVALVALTHRTHRTYRGLUGLY
8   LYSHISASNHISASPLEUPROALA

Entity 2, ZINC_ION - Zn - 65.409 Da.

1   ZN

Entity 3, W-box_DNA_chain_1 - Formula weight is not available

1   DCDGDCDCDTDTDTDGDADC
2   DCDADGDCDGDC

Entity 4, W-box_DNA_chain_2 - Formula weight is not available

1   DGDCDGDCDTDGDGDTDCDA
2   DADADGDGDCDG

Samples:

sample_1: WRKY_domain0.4 – 1.0 mM; W-box DNA chain 10.4 – 1.0 mM; W-box DNA chain 20.4 – 1.0 mM; potassium phosphate 20 mM; potassium chloride 200 mM; zinc chloride 20 uM; DTT, [U-2H], 1 mM; DSS 50 uM; H2O 95%; D2O 5%

sample_2: WRKY_domain0.4 – 1.0 mM; W-box DNA chain 10.4 – 1.0 mM; W-box DNA chain 20.4 – 1.0 mM; potassium phosphate 20 mM; potassium chloride 200 mM; zinc chloride 20 uM; DTT, [U-2H], 1 mM; DSS 50 uM; H2O 95%; D2O 5%

sample_2d: WRKY domain, [U-13C; U-15N], 0.4 – 1.0 mM; W-box DNA chain 10.4 – 1.0 mM; W-box DNA chain 20.4 – 1.0 mM; potassium phosphate 20 mM; potassium chloride 200 mM; zinc chloride 20 uM; DTT, [U-2H], 1 mM; DSS 50 uM; D2O 100%

sample_3: WRKY domain, [U-15N], 0.4 – 1.0 mM; W-box DNA chain 1, [U-15N]-T, 0.4 – 1.0 mM; W-box DNA chain 2, [U-15N]-T, 0.4 – 1.0 mM; potassium phosphate 20 mM; potassium chloride 200 mM; zinc chloride 20 uM; DTT, [U-2H], 1 mM; DSS 50 uM; D2O 5%; H2O 95%

sample_3p: WRKY domain, [U-15N], 0.4 – 1.0 mM; W-box DNA chain 1, [U-15N]-T, 0.4 – 1.0 mM; W-box DNA chain 2, [U-15N]-T, 0.4 – 1.0 mM; potassium phosphate 20 mM; potassium chloride 200 mM; zinc chloride 20 uM; DTT, [U-2H], 1 mM; DSS 50 uM; Pf1 phage 12 mg/mL; D2O 5%; H2O 95%

sample_conditions_1: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 283 K

sample_conditions_3: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2disotropicsample_conditions_2
2D 1H-15N HSQCsample_3isotropicsample_conditions_3
2D 1H-15N IPAP-HSQCsample_3isotropicsample_conditions_3
2D 1H-15N HSQCsample_3panisotropicsample_conditions_3
2D 1H-15N IPAP-HSQCsample_3panisotropicsample_conditions_3

Software:

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

FELIX v2000, Accelrys Software Inc. - data analysis

TALOS+, Shen, Delaglio, Cornilescu, Bax - data analysis

NMR spectrometers:

  • Bruker DMX 750 MHz
  • Bruker DMX 500 MHz

Related Database Links:

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