› 1h88

X-ray diffraction
2.8Å resolution

CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1

Released:
DOI: 10.2210/pdb1h88/pdb
PDB entry 1h88 coloured by chain, front view.
PDB entry 1h88 coloured by chain, side view.
PDB entry 1h88 coloured by chain, top view.
Source organisms:
Primary publication:
Mechanism of c-Myb-C/EBP beta cooperation from separated sites on a promoter.
Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M, Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A, Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K
Cell 108 57-70 (2002)
PMID: 11792321

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113885 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
CCAAT/enhancer-binding protein beta Chains: A, B
Molecule details ›
Chains: A, B
Length: 78 amino acids
Theoretical weight: 9.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P17676 (Residues: 259-336; Coverage: 23%)
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
Transcriptional activator Myb Chain: C
Molecule details ›
Chain: C
Length: 159 amino acids
Theoretical weight: 19.17 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06876 (Residues: 35-193; Coverage: 25%)
Gene name: Myb
Sequence domains: Myb-like DNA-binding domain
Structure domains: Homeodomain-like
DNA(5'-(*GP*AP*TP*GP*TP*GP*GP*CP*GP*CP*AP* AP*TP*CP*CP*TP*TP*AP*AP*CP*GP*GP*AP*CP*TP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 26 nucleotides
Theoretical weight: 8.03 KDa
DNA(5'-(*CP*CP*AP*GP*TP*CP*CP*GP*TP*TP*AP* AP*GP*GP*AP*TP*TP*GP*CP*GP*CP*CP*AP*CP*AP*T)-3') Chain: E
Molecule details ›
Chain: E
Length: 26 nucleotides
Theoretical weight: 7.95 KDa

Ligands and Environments

1 bound ligand:
Ligand NH4 1 x NH4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL45XU
Spacegroup: P21
Unit cell:
a: 41.735Å b: 156.966Å c: 55.868Å
α: 90° β: 100.16° γ: 90°
R-values:
R R work R free
0.222 0.222 0.277
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

12 review citations

CCAAT/enhancer-binding proteins: structure, function and regulation.
Ramji et al. (2002)
11 more

18 mentions without citation

Bis-histidine-coordinated hemes in four-helix bundles: how the geometry of the bundle controls the axial imidazole plane orientations in transmembrane cytochromes of mitochondrial complexes II and III and related proteins.
Berry et al. (2008)
17 more