› 4hc9

X-ray diffraction
1.6Å resolution

DNA binding by GATA transcription factor-complex 3

Released:
DOI: 10.2210/pdb4hc9/pdb
PDB entry 4hc9 coloured by chain, front view.
PDB entry 4hc9 coloured by chain, side view.
PDB entry 4hc9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation.
Chen Y, Bates DL, Dey R, Chen PH, Machado AC, Laird-Offringa IA, Rohs R, Chen L
Cell Rep 2 1197-206 (2012)
PMID: 23142663

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-117579 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Trans-acting T-cell-specific transcription factor GATA-3 Chain: A
Molecule details ›
Chain: A
Length: 115 amino acids
Theoretical weight: 12.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P23771 (Residues: 260-370; Coverage: 25%)
Gene name: GATA3
Sequence domains: GATA zinc finger
Structure domains: Erythroid Transcription Factor GATA-1, subunit A
DNA (5'-D(*TP*TP*CP*CP*TP*AP*AP*AP*TP*CP*AP*GP*AP*GP*AP*TP*AP*AP*CP*C)-3') Chain: Y
Molecule details ›
Chain: Y
Length: 20 nucleotides
Theoretical weight: 6.09 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*AP*AP*GP*GP*TP*TP*AP*TP*CP*TP*CP*TP*GP*AP*TP*TP*TP*AP*GP*G)-3') Chain: Z
Molecule details ›
Chain: Z
Length: 20 nucleotides
Theoretical weight: 6.18 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: C2
Unit cell:
a: 126.118Å b: 30.352Å c: 72.475Å
α: 90° β: 98.59° γ: 90°
R-values:
R R work R free
0.181 0.181 0.216
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

13 review citations

Absence of a simple code: how transcription factors read the genome.
Slattery et al. (2014)
12 more

10 mentions without citation

Structural Features of Transcription Factors Associating with Nucleosome Binding.
Fernandez Garcia et al. (2019)
9 more