› 3qmc

X-ray diffraction
2.1Å resolution

Structural Basis of Selective Binding of Nonmethylated CpG Islands by the CXXC Domain of CFP1

Released:
DOI: 10.2210/pdb3qmc/pdb
PDB entry 3qmc coloured by chain, front view.
PDB entry 3qmc coloured by chain, side view.
PDB entry 3qmc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain.
Xu C, Bian C, Lam R, Dong A, Min J
Nat Commun 2 227 (2011)
PMID: 21407193

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116772 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
CXXC-type zinc finger protein 1 Chain: A
Molecule details ›
Chain: A
Length: 79 amino acids
Theoretical weight: 9.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9P0U4 (Residues: 161-222; Coverage: 10%)
Gene names: CFP1, CGBP, CXXC1, PCCX1, PHF18
Sequence domains: CXXC zinc finger domain
5'-D(*GP*CP*CP*AP*CP*CP*GP*CP*TP*GP*GP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*GP*CP*CP*AP*GP*CP*GP*GP*TP*GP*GP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2221
Unit cell:
a: 30.545Å b: 75.016Å c: 126.282Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.214 0.249
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

28 review citations

Role of TET enzymes in DNA methylation, development, and cancer.
Rasmussen et al. (2016)
27 more

3 mentions without citation

Polycomb-like proteins link the PRC2 complex to CpG islands.
Li et al. (2017)
2 more