› 6ir8

X-ray diffraction
2.3Å resolution

Rice WRKY/DNA complex

Released:
DOI: 10.2210/pdb6ir8/pdb
PDB entry 6ir8 coloured by chain, front view.
PDB entry 6ir8 coloured by chain, side view.
PDB entry 6ir8 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain.
Cheng X, Zhao Y, Jiang Q, Yang J, Zhao W, Taylor IA, Peng YL, Wang D, Liu J
Nucleic Acids Res 47 4308-4318 (2019)
PMID: 30783673

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110817 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
WRKY domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 69 amino acids
Theoretical weight: 8.16 KDa
Source organism: Oryza sativa Japonica Group
Expression system: Escherichia coli
UniProt:
  • Canonical: B9FNW2 (Residues: 128-196; Coverage: 20%)
Gene name: OsJ_18062
Sequence domains: WRKY DNA -binding domain
DNA (5'-D(P*GP*AP*TP*AP*TP*TP*TP*GP*AP*CP*CP*GP*GP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.32 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*TP*CP*CP*GP*GP*TP*CP*AP*AP*AP*TP*AP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.24 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2221
Unit cell:
a: 48.225Å b: 87.831Å c: 99.691Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.193 0.244
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

WRKY transcription factors and plant defense responses: latest discoveries and future prospects.
Wani et al. (2021)
3 more

2 mentions without citation

Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain.
Cheng et al. (2019)
1 more