› 3f27

X-ray diffraction
2.75Å resolution

Structure of Sox17 Bound to DNA

Released:
DOI: 10.2210/pdb3f27/pdb
PDB entry 3f27 coloured by chain, front view.
PDB entry 3f27 coloured by chain, side view.
PDB entry 3f27 coloured by chain, top view.
Source organisms:
Primary publication:
The structure of Sox17 bound to DNA reveals a conserved bending topology but selective protein interaction platforms.
Palasingam P, Jauch R, Ng CK, Kolatkar PR
J Mol Biol 388 619-30 (2009)
PMID: 19328208

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116234 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcription factor SOX-17 Chain: D
Molecule details ›
Chain: D
Length: 83 amino acids
Theoretical weight: 10.08 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q61473 (Residues: 66-144; Coverage: 19%)
Gene names: Sox-17, Sox17
Sequence domains: HMG (high mobility group) box
Structure domains: High mobility group box domain
DNA (5'-D(*DGP*DTP*DCP*DTP*DCP*DTP*DAP*DTP*DTP*DGP*DTP*DCP*DCP*DTP*DGP*DG)-3') Chain: A
Molecule details ›
Chain: A
Length: 16 nucleotides
Theoretical weight: 4.87 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*DCP*DCP*DAP*DGP*DGP*DAP*DCP*DAP*DAP*DTP*DAP*DGP*DAP*DGP*DAP*DC)-3') Chain: B
Molecule details ›
Chain: B
Length: 16 nucleotides
Theoretical weight: 4.93 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P3221
Unit cell:
a: 68.753Å b: 68.753Å c: 66.329Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.243 0.242 0.265
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

7 review citations

Origins of specificity in protein-DNA recognition.
Rohs et al. (2010)
6 more

14 mentions without citation

The high mobility group box: the ultimate utility player of a cell.
Malarkey et al. (2012)
13 more