› 6od5

X-ray diffraction
2.05Å resolution

Human TCF4 C-terminal bHLH domain in Complex with 12-bp Oligonucleotide Containing E-box Sequence with 5-carboxylcytosines

Released:
DOI: 10.2210/pdb6od5/pdb
PDB entry 6od5 coloured by chain, front view.
PDB entry 6od5 coloured by chain, side view.
PDB entry 6od5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine.
Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal RM, Cheng X
Nucleic Acids Res 47 8375-8387 (2019)
PMID: 31081034

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120380 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Transcription factor 4 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 62 amino acids
Theoretical weight: 7.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P15884 (Residues: 565-624; Coverage: 9%)
Gene names: BHLHB19, ITF2, SEF2, TCF4
Sequence domains: Helix-loop-helix DNA-binding domain
Structure domains: Helix-loop-helix DNA-binding domain
DNA (5'-D(*AP*(1CC)P*GP*CP*AP*CP*GP*TP*GP*(1CC)P*G)-3') Chains: E, F, X, Y
Molecule details ›
Chains: E, F, X, Y
Length: 12 nucleotides
Theoretical weight: 3.75 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand EDO 5 x EDO
Ligand CL 1 x CL
Ligand GOL 1 x GOL
1 modified residue:
Ligand 1CC 8 x 1CC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P1
Unit cell:
a: 44.677Å b: 44.757Å c: 54.64Å
α: 78.63° β: 78.88° γ: 79.27°
R-values:
R R work R free
0.236 0.234 0.28
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

7 review citations

Transcription factor 4 and its association with psychiatric disorders.
Teixeira et al. (2021)
6 more

1 mention without citation

Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine.
Yang et al. (2019)