› 5k5j

X-ray diffraction
2.29Å resolution

Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P41212

Released:
DOI: 10.2210/pdb5k5j/pdb
PDB entry 5k5j coloured by chain, front view.
PDB entry 5k5j coloured by chain, side view.
PDB entry 5k5j 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-118893 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcriptional repressor CTCF Chain: A
Molecule details ›
Chain: A
Length: 117 amino acids
Theoretical weight: 13.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49711 (Residues: 378-489; Coverage: 15%)
Gene name: CTCF
Sequence domains: Zinc finger, C2H2 type
DNA (5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*GP*CP*AP*AP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.91 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*TP*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 4.03 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand SO4 1 x SO4
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P41212
Unit cell:
a: 58.903Å b: 58.903Å c: 172.264Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.254
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

27 review citations

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

2 mentions without citation

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Hashimoto et al. (2017)
1 more