› 6t78

X-ray diffraction
2.5Å resolution

Structure of human Sox11 transcription factor in complex with a short DNA fragment

Released:
DOI: 10.2210/pdb6t78/pdb
PDB entry 6t78 coloured by chain, front view.
PDB entry 6t78 coloured by chain, side view.
PDB entry 6t78 coloured by chain, top view.
Source organisms:
Primary publication:
Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.
Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P
Nature 580 669-672 (2020)
PMID: 32350470

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-120629 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcription factor SOX-11 Chains: A, B
Molecule details ›
Chains: A, B
Length: 109 amino acids
Theoretical weight: 12.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P35716 (Residues: 33-138; Coverage: 24%)
Gene name: SOX11
Sequence domains: HMG (high mobility group) box
DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 16 nucleotides
Theoretical weight: 4.89 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*A)-3') Chains: D, G
Molecule details ›
Chains: D, G
Length: 16 nucleotides
Theoretical weight: 4.9 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: SLS BEAMLINE X10SA
Spacegroup: P61
Unit cell:
a: 106.13Å b: 106.13Å c: 76.89Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.228 0.227 0.258
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

24 review citations

Pioneer Transcription Factors Initiating Gene Network Changes.
Zaret KS. (2020)
23 more

2 mentions without citation

SOX11 Inhibitors Are Cytotoxic in Mantle Cell Lymphoma.
Jatiani et al. (2021)
1 more