› 5yeg

X-ray diffraction
2Å resolution

Crystal structure of CTCF ZFs4-8-Hs5-1a complex

Released:
DOI: 10.2210/pdb5yeg/pdb
PDB entry 5yeg coloured by chain, front view.
PDB entry 5yeg coloured by chain, side view.
PDB entry 5yeg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites.
Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang Y
Cell Res 27 1365-1377 (2017)
PMID: 29076501

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-218997 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Transcriptional repressor CTCF Chain: A
Molecule details ›
Chain: A
Length: 142 amino acids
Theoretical weight: 16.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P49711 (Residues: 349-490; Coverage: 20%)
Gene name: CTCF
Sequence domains: Zinc finger, C2H2 type
Transcriptional repressor CTCF Chain: B
Molecule details ›
Chain: B
Length: 141 amino acids
Theoretical weight: 16.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P49711 (Residues: 349-489; Coverage: 19%)
Gene name: CTCF
Sequence domains: Zinc finger, C2H2 type
DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*GP*CP*TP*GP*GP*TP*TP*AP*AP*AP*G)-3') Chains: D, E
Molecule details ›
Chains: D, E
Length: 21 nucleotides
Theoretical weight: 6.41 KDa
DNA (5'-D(*AP*CP*TP*TP*TP*AP*AP*CP*CP*AP*GP*CP*AP*GP*AP*GP*GP*GP*CP*G)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 20 nucleotides
Theoretical weight: 6.17 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 10 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P1
Unit cell:
a: 46.167Å b: 56.502Å c: 67.486Å
α: 78.41° β: 79.31° γ: 78.6°
R-values:
R R work R free
0.187 0.186 0.204
Expression system: Escherichia coli K-12

Quick links

Citations

15 review citations

Genome folding through loop extrusion by SMC complexes.
Davidson et al. (2021)
14 more

1 mention without citation

Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites.
Yin et al. (2017)