› 4s2q

X-ray diffraction
2.7Å resolution

Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element

Released:
DOI: 10.2210/pdb4s2q/pdb
PDB entry 4s2q coloured by chain, front view.
PDB entry 4s2q coloured by chain, side view.
PDB entry 4s2q coloured by chain, top view.
Source organisms:
Entry authors: Vivekanandan S, Moovarkumudalvan B, Lescar J, Kolatkar PR

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-118159 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcription factor SOX-9 Chain: D
Molecule details ›
Chain: D
Length: 76 amino acids
Theoretical weight: 9.26 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q04887 (Residues: 103-178; Coverage: 15%)
Gene names: Sox-9, Sox9
Sequence domains: HMG (high mobility group) box
Structure domains: High mobility group box domain
DNA (5'-D(P*AP*GP*GP*CP*TP*TP*TP*GP*TP*TP*CP*TP*CP*CP*TP*G)-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(P*AP*GP*GP*AP*GP*AP*AP*CP*AP*AP*AP*GP*CP*CP*TP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 16 nucleotides
Theoretical weight: 4.97 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: NSLS BEAMLINE X29A
Spacegroup: P41212
Unit cell:
a: 99.492Å b: 99.492Å c: 45.894Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.213 0.269
Expression systems:
  • Escherichia coli
  • Not provided

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