› 5yeh

X-ray diffraction
2.33Å resolution

Crystal structure of CTCF ZFs4-8-eCBS

Released:
DOI: 10.2210/pdb5yeh/pdb
PDB entry 5yeh coloured by chain, front view.
PDB entry 5yeh coloured by chain, side view.
PDB entry 5yeh coloured by chain, top view.
Source organisms:
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-119433 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcriptional repressor CTCF Chains: A, B
Molecule details ›
Chains: A, B
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
DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*CP*CP*GP*CP*TP*AP*GP*AP*GP*GP*GP*CP*G)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 20 nucleotides
Theoretical weight: 6.19 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*AP*GP*CP*GP*GP*AP*AP*AP*CP*CP*G)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 20 nucleotides
Theoretical weight: 6.08 KDa
Source organism: synthetic construct
Expression system: Not provided

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: 45.845Å b: 54.876Å c: 66.938Å
α: 81.17° β: 80.11° γ: 79.72°
R-values:
R R work R free
0.224 0.222 0.27
Expression systems:
  • Escherichia coli K-12
  • Not provided

Quick links

Citations

15 review citations

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

3 mentions without citation

Chemical Decorations of "MARs" Residents in Orchestrating Eukaryotic Gene Regulation.
Roychowdhury et al. (2020)
2 more