PDBe 1io4

X-ray diffraction
3Å resolution

CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA CORE DOMAIN HETERODIMER AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
Core-binding factor subunit beta Chain: D
Molecule details ›
Chain: D
Length: 141 amino acids
Theoretical weight: 16.61 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08024 (Residues: 1-141; Coverage: 75%)
Gene names: Cbfb, Pebp2b, Pebpb2
Structure domains: Core binding factor beta, CBF
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
Runt-related transcription factor 1 Chain: C
Molecule details ›
Chain: C
Length: 123 amino acids
Theoretical weight: 13.72 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q03347 (Residues: 60-182; Coverage: 27%)
Gene names: Aml1, Cbfa2, Pebp2ab, Runx1
Structure domains: Immunoglobulin-like
CSF-1R PROMOTER Chain: E
Molecule details ›
Chain: E
Length: 26 nucleotides
Theoretical weight: 8.02 KDa
CSF-1R PROMOTER Chain: F
Molecule details ›
Chain: F
Length: 26 nucleotides
Theoretical weight: 7.96 KDa

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL45XU
Spacegroup: C2221
Unit cell:
a: 121.108Å b: 163.6Å c: 109.326Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.247 0.247 0.299
Expression system: Escherichia coli BL21(DE3)