› 6mg1

X-ray diffraction
1.75Å resolution

C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide Containing Consensus Recognition Sequence-C2 Crystal Form

Released:
DOI: 10.2210/pdb6mg1/pdb
PDB entry 6mg1 coloured by chain, front view.
PDB entry 6mg1 coloured by chain, side view.
PDB entry 6mg1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for effects of CpA modifications on C/EBPβ binding of DNA.
Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X
Nucleic Acids Res 47 1774-1785 (2019)
PMID: 30566668

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120285 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
CCAAT/enhancer-binding protein beta Chains: A, B
Molecule details ›
Chains: A, B
Length: 78 amino acids
Theoretical weight: 9.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P17676 (Residues: 269-344; Coverage: 22%)
Gene names: CEBPB, PP9092, TCF5
Sequence domains: Basic region leucine zipper
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
16-bp methylated oligonucleotide Chains: C, D
Molecule details ›
Chains: C, D
Length: 16 nucleotides
Theoretical weight: 4.92 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand EDO 4 x EDO
Ligand GOL 1 x GOL
1 modified residue:
Ligand 5CM 4 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-003
Spacegroup: C2
Unit cell:
a: 48.11Å b: 77.405Å c: 99.825Å
α: 90° β: 103.9° γ: 90°
R-values:
R R work R free
0.216 0.214 0.25
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors.
Kribelbauer et al. (2020)
2 more

4 mentions without citation

Structural basis for effects of CpA modifications on C/EBPβ binding of DNA.
Yang et al. (2019)
3 more