› 5yef

X-ray diffraction
2.81Å resolution

Crystal structure of CTCF ZFs2-8-Hs5-1aE

Released:
DOI: 10.2210/pdb5yef/pdb
PDB entry 5yef coloured by chain, front view.
PDB entry 5yef coloured by chain, side view.
PDB entry 5yef 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-119431 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcriptional repressor CTCF Chains: A, B, G, J
Molecule details ›
Chains: A, B, G, J
Length: 199 amino acids
Theoretical weight: 23.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49711 (Residues: 292-490; Coverage: 27%)
Gene name: CTCF
Sequence domains: Zinc finger, C2H2 type
DNA (27-MER) Chains: C, E, H, K
Molecule details ›
Chains: C, E, H, K
Length: 27 nucleotides
Theoretical weight: 8.27 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (27-MER) Chains: D, F, I, L
Molecule details ›
Chains: D, F, I, L
Length: 28 nucleotides
Theoretical weight: 8.64 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 24 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 90.115Å b: 143.064Å c: 90.233Å
α: 90° β: 119.69° γ: 90°
R-values:
R R work R free
0.225 0.224 0.254
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

15 review citations

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

6 mentions without citation

Global reference mapping of human transcription factor footprints.
Vierstra et al. (2020)
5 more