› 3qmi

X-ray diffraction
2.1Å resolution

Structural Basis of Selective Binding of Non-Methylated CpG islands (DNA-ACGT) by the CXXC Domain of CFP1

Released:
DOI: 10.2210/pdb3qmi/pdb
PDB entry 3qmi coloured by chain, front view.
PDB entry 3qmi coloured by chain, side view.
PDB entry 3qmi 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-116776 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 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
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*AP*CP*GP*TP*TP*GP*GP*C)-3' Chains: B, C
Molecule details ›
Chains: B, C
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand PEG 2 x PEG
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2221
Unit cell:
a: 30.624Å b: 75.009Å c: 125.905Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.207 0.258
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

28 review citations

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

2 mentions without citation

The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain.
Xu et al. (2011)
1 more