› 3u2b

X-ray diffraction
2.4Å resolution

Structure of the Sox4 HMG domain bound to DNA

Released:
DOI: 10.2210/pdb3u2b/pdb
PDB entry 3u2b coloured by chain, front view.
PDB entry 3u2b coloured by chain, side view.
PDB entry 3u2b coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition.
Jauch R, Ng CK, Narasimhan K, Kolatkar PR
Biochem J 443 39-47 (2012)
PMID: 22181698

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-116952 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcription factor SOX-4 Chain: C
Molecule details ›
Chain: C
Length: 79 amino acids
Theoretical weight: 9.72 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q06831 (Residues: 57-135; Coverage: 18%)
Gene names: Sox-4, Sox4
Sequence domains: HMG (high mobility group) box
Structure domains: High mobility group box domain
DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*GP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 16 nucleotides
Theoretical weight: 4.87 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 16 nucleotides
Theoretical weight: 4.93 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P3221
Unit cell:
a: 69.941Å b: 69.941Å c: 63.205Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.27 0.235 0.28
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

The role of SRY-related HMG box transcription factor 4 (SOX4) in tumorigenesis and metastasis: friend or foe?
Vervoort et al. (2013)
9 more

13 mentions without citation

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