› 3cmy

X-ray diffraction
1.95Å resolution

Structure of a homeodomain in complex with DNA

Released:
DOI: 10.2210/pdb3cmy/pdb
PDB entry 3cmy coloured by chain, ensemble of 2 models, front view.
PDB entry 3cmy coloured by chain, ensemble of 2 models, side view.
PDB entry 3cmy coloured by chain, ensemble of 2 models, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for DNA recognition by the human PAX3 homeodomain.
Birrane G, Soni A, Ladias JA
Biochemistry 48 1148-55 (2009)
PMID: 19199574

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116144 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Paired box protein Pax-3 Chain: A
Molecule details ›
Chain: A
Length: 61 amino acids
Theoretical weight: 7.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P23760 (Residues: 219-278; Coverage: 13%)
Gene names: HUP2, PAX3
Sequence domains: Homeodomain
Structure domains: Homeodomain-like
5'-D(*DAP*DCP*DAP*DTP*DAP*DAP*DP*DCP*DGP*DAP*DTP*DTP*DAP*DC)-3' Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.25 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*DTP*DGP*DTP*DAP*DAP*DTP*DCP*DGP*DAP*DTP*DTP*DAP*DTP*DG)-3' Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.31 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12B
Spacegroup: C2221
Unit cell:
a: 43.325Å b: 62.243Å c: 92.556Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.172 0.213
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Review and update of mutations causing Waardenburg syndrome.
Pingault et al. (2010)
3 more

8 mentions without citation

Molecular Modeling the Proteins from the exo-xis Region of Lambda and Shigatoxigenic Bacteriophages.
Donaldson LW. (2021)
7 more