› 6j9c

X-ray diffraction
3.1Å resolution

Crystal structure of Arabidopsis thaliana transcription factor LEC2-DNA complex

Released:
DOI: 10.2210/pdb6j9c/pdb
PDB entry 6j9c coloured by chain, front view.
PDB entry 6j9c coloured by chain, side view.
PDB entry 6j9c coloured by chain, top view.
Source organisms:
Primary publication:
Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis.
Tao Z, Hu H, Luo X, Jia B, Du J, He Y
Nat Plants 5 424-435 (2019)
PMID: 30962525

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120060 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
B3 domain-containing transcription factor LEC2 Chains: A, D
Molecule details ›
Chains: A, D
Length: 123 amino acids
Theoretical weight: 14.31 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q1PFR7 (Residues: 160-273; Coverage: 31%)
Gene names: At1g28300, F3H9.5, LEC2
Sequence domains: B3 DNA binding domain
Structure domains: DNA-binding pseudobarrel domain
DNA (5'-D(*GP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 15 nucleotides
Theoretical weight: 4.62 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 15 nucleotides
Theoretical weight: 4.56 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P21212
Unit cell:
a: 71.073Å b: 96.601Å c: 99.263Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.225 0.257
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

12 review citations

Wheat genomic study for genetic improvement of traits in China.
Xiao et al. (2022)
11 more

2 mentions without citation

Structural variation affecting DNA backbone interactions underlies adaptation of B3 DNA binding domains to constraints imposed by protein architecture.
Jia et al. (2021)
1 more