› 5t0u

X-ray diffraction
3.2Å resolution

CTCF ZnF2-7 and DNA complex structure

Released:
DOI: 10.2210/pdb5t0u/pdb
PDB entry 5t0u coloured by chain, front view.
PDB entry 5t0u coloured by chain, side view.
PDB entry 5t0u coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X
Mol Cell 66 711-720.e3 (2017)
PMID: 28529057

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-119129 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcriptional repressor CTCF Chains: A, D
Molecule details ›
Chains: A, D
Length: 177 amino acids
Theoretical weight: 20.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P49711 (Residues: 294-465; Coverage: 24%)
Gene name: CTCF
Sequence domains: Zinc finger, C2H2 type
DNA (5'-D(*CP*CP*TP*CP*AP*CP*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 23 nucleotides
Theoretical weight: 6.91 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*AP*GP*TP*GP*AP*GP*G)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 23 nucleotides
Theoretical weight: 7.21 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 12 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P2
Unit cell:
a: 101.63Å b: 40.96Å c: 106.67Å
α: 90° β: 92.21° γ: 90°
R-values:
R R work R free
0.231 0.23 0.266
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

26 review citations

Dynamic DNA methylation: In the right place at the right time.
Luo et al. (2018)
25 more

8 mentions without citation

Structural insights into DNA loop extrusion by SMC protein complexes.
Datta et al. (2020)
7 more