BMRB Entry 17732

Name: Complex of the C-terminal WRKY domain of AtWRKY4 and a W-box DNA
Published: 2012-01-18

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PDB ID: 2lex
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17732
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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

Deposition date: 2011-06-24 Original release date: 2012-01-18

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:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	70
15N chemical shifts	80
1H chemical shifts	662

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	WRKY_domain	1
2	ZINC_ION	2
3	W-box_DNA_chain_1	3
4	W-box_DNA_chain_2	4

Entities:

Entity 1, WRKY_domain 78 residues - 7208.253 Da.

1

GLY

SER

GLY

SER

GLY

VAL

GLN

THR

2

THR

SER

GLU

VAL

ASP

LEU

ASP

GLY

3

TYR

ARG

TRP

ARG

LYS

TYR

GLY

GLN

LYS

VAL

4

VAL

LYS

GLY

ASN

PRO

TYR

PRO

ARG

SER

TYR

5

TYR

LYS

CYS

THR

PRO

GLY

CYS

GLY

VAL

6

ARG

LYS

HIS

VAL

GLU

ARG

ALA

THR

ASP

7

PRO

LYS

ALA

VAL

THR

TYR

GLU

GLY

8

LYS

HIS

ASN

HIS

ASP

LEU

PRO

ALA

Entity 2, ZINC_ION - Zn - 65.409 Da.

1

ZN

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

1

DC

DG

DC

DT

DG

DA

DC

2

DC

DA

DG

DC

DG

DC

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

1

DG

DC

DG

DC

DT

DG

DT

DC

DA

2

DA

DG

DC

DG

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2d	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_3
2D 1H-15N IPAP-HSQC	sample_3	isotropic	sample_conditions_3
2D 1H-15N HSQC	sample_3p	anisotropic	sample_conditions_3
2D 1H-15N IPAP-HSQC	sample_3p	anisotropic	sample_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

Biological Magnetic Resonance Data Bank