› 6lff

X-ray diffraction
1.79Å resolution

transcription factor SATB1 CUTr1 domain in complex with a phosphorothioate DNA

Released:
DOI: 10.2210/pdb6lff/pdb
PDB entry 6lff coloured by chain, front view.
PDB entry 6lff coloured by chain, side view.
PDB entry 6lff coloured by chain, top view.
Source organisms:
Primary publication:
Enhanced affinity of racemic phosphorothioate DNA with transcription factor SATB1 arising from diastereomer-specific hydrogen bonds and hydrophobic contacts.
Yamasaki K, Akutsu Y, Yamasaki T, Miyagishi M, Kubota T
Nucleic Acids Res 48 4551-4561 (2020)
PMID: 32187371

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-120219 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-binding protein SATB1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 93 amino acids
Theoretical weight: 10.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q01826 (Residues: 368-452; Coverage: 11%)
Gene name: SATB1
Sequence domains: CUT domain
DNA (5'-D(*GP*(C7R)P*(PST)P*AP*AP*TP*AP*TP*AP*TP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*AP*TP*(AS)P*(PST)P*(AS)P*(PST)P*TP*AP*GP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.73 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
3 modified residues:
Ligand C7R 1 x C7R
Ligand PST 3 x PST
Ligand AS 2 x AS

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P31
Unit cell:
a: 45.32Å b: 45.32Å c: 97.862Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.232 0.23 0.271
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Chemistry, structure and function of approved oligonucleotide therapeutics.
Egli et al. (2023)
1 more

1 mention without citation

Enhanced affinity of racemic phosphorothioate DNA with transcription factor SATB1 arising from diastereomer-specific hydrogen bonds and hydrophobic contacts.
Yamasaki et al. (2020)