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

X-ray diffraction
2.5Å resolution
PDB entry 3qmh coloured by chain, front view.
PDB entry 3qmh coloured by chain, side view.
PDB entry 3qmh coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero trimer (preferred)
Entry contents: 1 distinct polypeptide molecule
1 distinct DNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: CXXC-type zinc finger protein 1 and DNA
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Multimeric state: hetero trimer
Accessible surface area: 6936.44 Å2
Buried surface area: 2328.16 Å2
Dissociation area: 623.47 Å2
Dissociation energy (ΔGdiss): 2.37 kcal/mol
Dissociation entropy (TΔSdiss): 9.34 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116775

Macromolecules

CXXC-type zinc finger protein 1
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
Pfam: CXXC zinc finger domain
InterPro: Zinc finger, CXXC-type
CXXC-type zinc finger protein 1 in PDB entry 3qmh, assembly 1, front view.
CXXC-type zinc finger protein 1 in PDB entry 3qmh, assembly 1, side view.
CXXC-type zinc finger protein 1 in PDB entry 3qmh, assembly 1, top view.
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DNA chains B, C
Name: 5'-D(*GP*CP*CP*AP*TP*CP*GP*AP*TP*GP*GP*C)-3'
Representative chains: B, C
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
5'-D(*GP*CP*CP*AP*TP*CP*GP*AP*TP*GP*GP*C)-3' in PDB entry 3qmh, assembly 1, front view.
5'-D(*GP*CP*CP*AP*TP*CP*GP*AP*TP*GP*GP*C)-3' in PDB entry 3qmh, assembly 1, side view.
5'-D(*GP*CP*CP*AP*TP*CP*GP*AP*TP*GP*GP*C)-3' in PDB entry 3qmh, assembly 1, top view.
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