› 5k5l

X-ray diffraction
3.12Å resolution

Homo sapiens CCCTC-binding factor (CTCF) ZnF6-8 and H19 sequence DNA complex structure

Released:
DOI: 10.2210/pdb5k5l/pdb
PDB entry 5k5l coloured by chain, front view.
PDB entry 5k5l coloured by chain, side view.
PDB entry 5k5l 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 heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118894 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcriptional repressor CTCF Chains: E, F, G
Molecule details ›
Chains: E, F, G
Length: 93 amino acids
Theoretical weight: 10.9 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49711 (Residues: 405-492; Coverage: 12%)
Gene name: CTCF
Sequence domains: Zinc finger, C2H2 type
DNA (5'-D(*GP*TP*TP*GP*CP*CP*GP*CP*GP*TP*G)-3') Chains: A, C
Molecule details ›
Chains: A, C
Length: 11 nucleotides
Theoretical weight: 3.38 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*CP*GP*CP*GP*GP*CP*AP*AP*C)-3') Chains: B, D
Molecule details ›
Chains: B, D
Length: 11 nucleotides
Theoretical weight: 3.33 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 7 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21212
Unit cell:
a: 126.792Å b: 52.397Å c: 69.135Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.236 0.27
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