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- PDB-9m0k: Crystal structure of the WRKY DNA-binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9m0k
TitleCrystal structure of the WRKY DNA-binding domain in complex with the W-box DNA motif
Components
  • DNA (5'-D(P*TP*CP*TP*AP*GP*TP*CP*AP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*AP*TP*TP*GP*AP*CP*TP*AP*GP*A)-3')
  • WRKY17 transcription factor
KeywordsDNA BINDING PROTEIN/DNA / DNA recognition mechanism / Complex / Gene regulation / Binding specificity / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sequence-specific DNA binding / calmodulin binding / DNA-binding transcription factor activity / nucleus
Similarity search - Function
Zn-cluster domain / Plant zinc cluster domain / 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) / WRKY17 transcription factor
Similarity search - Component
Biological speciesGossypium hirsutum (cotton)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, Y.L. / Xiao, Q. / Shang, X.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271309 China
CitationJournal: Biochem.J. / Year: 2026
Title: Structural basis for sequence-specific DNA recognition by a group IId WRKY transcription factor GhWRKY17 in cotton.
Authors: Xiao, Q. / Wang, Y. / Shang, X. / Chen, Y. / Zhang, M. / Zhou, Y. / Huang, X. / Qin, S. / Min, J. / Xu, G. / Liu, Y.
History
DepositionFeb 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WRKY17 transcription factor
B: WRKY17 transcription factor
C: DNA (5'-D(P*TP*CP*TP*AP*GP*TP*CP*AP*AP*TP*CP*A)-3')
D: DNA (5'-D(P*TP*GP*AP*TP*TP*GP*AP*CP*TP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8396
Polymers22,7084
Non-polymers1312
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-22 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.111, 93.285, 83.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

21B-514-

HOH

31B-525-

HOH

41B-531-

HOH

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Components

#1: Protein WRKY17 transcription factor


Mass: 7692.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gossypium hirsutum (cotton) / Production host: Escherichia coli (E. coli) / References: UniProt: R9Q8W6
#2: DNA chain DNA (5'-D(P*TP*CP*TP*AP*GP*TP*CP*AP*AP*TP*CP*A)-3')


Mass: 3621.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Gossypium hirsutum (cotton)
#3: DNA chain DNA (5'-D(P*TP*GP*AP*TP*TP*GP*AP*CP*TP*AP*GP*A)-3')


Mass: 3701.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Gossypium hirsutum (cotton)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion / Details: 20% PEG 3350, 0.2 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.28149 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28149 Å / Relative weight: 1
ReflectionResolution: 1.8→46.81 Å / Num. obs: 19996 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.4
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.219 / Num. unique obs: 1105 / CC1/2: 0.895

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDS(1.20.1_4487: ???)data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.81 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2803 1952 9.77 %
Rwork0.247 --
obs0.247 19975 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 486 2 177 1639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d22.86593
X-RAY DIFFRACTIONf_chiral_restr0.057218
X-RAY DIFFRACTIONf_plane_restr0.01194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.32551320.29221221X-RAY DIFFRACTION97
1.84-1.890.31421340.29111256X-RAY DIFFRACTION100
1.89-1.950.31991560.28011286X-RAY DIFFRACTION100
1.95-2.010.34771180.2741275X-RAY DIFFRACTION100
2.01-2.080.31981280.28271293X-RAY DIFFRACTION100
2.08-2.170.32321230.26851313X-RAY DIFFRACTION100
2.17-2.270.33111300.26691279X-RAY DIFFRACTION100
2.27-2.380.31431130.25351296X-RAY DIFFRACTION100
2.38-2.530.29821610.25741273X-RAY DIFFRACTION100
2.53-2.730.29591450.26491290X-RAY DIFFRACTION100
2.73-30.29691690.24971276X-RAY DIFFRACTION100
3-3.440.24861510.22381264X-RAY DIFFRACTION98
3.44-4.330.23551320.18551333X-RAY DIFFRACTION100
4.33-46.810.21451600.1881368X-RAY DIFFRACTION99

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